Photobioreactor

ABSTRACT

Provided herein is a transgenic bacteria engineered to accumulate carbohydrates, for example disaccharides. Also provided is a photobioreactor for cultivating photosynthetic microorganisms comprising a non-gelatinous, solid cultivation support suitable for providing nutrients and moisture to photosynthetic microorganisms and a physical barrier covering at least a portion of the surface of the cultivation support. Devices for the large scale and continuous cultivation of photosynthetic microorganisms incorporating photobioreactors and methods of use are disclosed. Also disclosed are methods of producing fermentable sugar from photosynthetic microorganisms using a photobioreactor of the invention.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. application Ser. No.14/272,420 filed 7 May 2014; which is a continuation of U.S. applicationSer. No. 13/737,201 filed 9 Jan. 2013, now U.S. Pat. No. 8,728,783issued 20 May 2014; which is a Divisional of U.S. application Ser. No.12/348,887 filed 5 Jan. 2009, now U.S. Pat. No. 8,367,379 issued 5 Feb.2013; which claims priority to U.S. Provisional Application Ser. Nos.61/085,797 filed 1 Aug. 2008 and 61/018,798 filed 3 Jan. 2008; each ofwhich is incorporated herein by reference in its entirety.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED IN COMPUTER READABLEFORM

The Sequence Listing, which is a part of the present disclosure,includes a computer readable form and a written sequence listingcomprising nucleotide and/or amino acid sequences of the presentinvention. The sequence listing information recorded in computerreadable form is identical to the written sequence listing. The subjectmatter of the Sequence Listing is incorporated herein by reference inits entirety.

FIELD OF THE INVENTION

The present invention generally relates to transgenic microorganisms andmethods and devices for their cultivation.

BACKGROUND

To address the world's increasing energy requirements, efficient andenvironmentally sound alternatives to the use of fossil fuels are soughtafter. Alternative fuels, such as ethanol or biodiesel, can be producedfrom plant biomass. For example, the key ingredient used to produceethanol from current processes is termed fermentable sugar. Most often,fermentable sugar is in the form of sucrose, glucose, or high-fructosecorn syrup. Plants currently grown to produce such biomass include corn,sugarcane, soybeans, canola, jatropha, and so forth. But much of theplant biomass used to produce fermentable sugar requires extensiveenergy-intensive pre-processing. Further, use of such plant biomass canlead to soil depletion, erosion, and diversion of the food supply.

It is known that some cyanobacteria produce sucrose through the actionof sucrose phosphate synthase and sucrose phosphate phosphatase, whereit has been studied exclusively as an osmoprotectant. With respect tosalt tolerance, cyanobacteria can be divided into three groups. Strainshaving low tolerance (less than 700 mM) synthesize either sucrose, as isthe case with Synechococcus elongatus PCC 7942, or another dissaccharideknown as trehalose [Blumwald et al., Proc Natl Acd Sci USA (1983)80:2599-2602 and Reed et al., FEMS Microbiol Rev (1986) 39:51-56].Glucosylglycerol is produced by strains having moderate halotolerance(0.7-1.8 mM), such as Synechocystis sp. PCC 6803. High salt tolerance(up to 2.5 M) results from the accumulation of either glycine betaine orglutamate betaine. Miao et al. [FEMS Microbiol Lett (2003) 218:71-77]determined that when glucosylglycerol biosynthesis is blocked bydeletion of the agp gene, however, Synechocystis sp. PCC 6803 producessucrose as its osmoprotectant. Desiccation tolerant cyanobacteria alsoproduce sucrose and trehalose in response to matric water stress[Hershkovitz et al., Appl Environ Microbiol (1991) 57:645-648].

Synechocystis spp. PCC 6803 (ATCC 27184) and Synechococcus elongatus PCC7942 (ATCC 33912) are relatively well-studied, have genetic toolsavailable and the sequences of their genomes are known (see e.g.,Koksharova, O. A. and Wolk, C. P. 2002. Appl Microbiol Biotechnol 58,123-137; Ikeuchil, M. and Satoshi Tabata, S. 2001. PhotosynthesisResearch 70, 73-83; Golden, S. S., Brusslan, J. and Haselkorn, R. 1987.Methods in Enzymology 153, 215-231; Friedberg, D. 1988. Methods inEnzymology 167, 736-747; Kaneko, T. et al. 1996. DNA Research 3,109-136).

The commercial cultivation of photosynthetic microorganisms such asSpirulina maximum, Spirulina platensis, Dunaliella salina, Botrycoccusbraunii, Chlorella vulgaris, Chlorella pyrenoidosa, Serenastrumcapricomutum, Scenedesmus auadricauda, Porphyridium cruentum,Scenedesmus acutus, Dunaliella sp., Scenedesmus obliquus, Anabaenopsis,Aulosira, Cylindrospermum, Scenecoccus sp., Scenecosystis sp., andTolypothrix is desirable for numerous applications including theproduction of fine chemicals, pharmaceuticals, cosmetic pigments, fattyacids, antioxidants, proteins with prophylactic action, growth factors,antibiotics, vitamins and polysaccharides. The algic biomass can also beuseful, in a low dose, to replace or decrease the level of antibioticsin animal food or be useful as a source of proteins. Furthermore, thealgic biomass provided in a wet form, as opposed to a dried form, can befermented or liquefied by thermal processes to produce fuel. Thus, thereis great interest in the ability to increase the efficiency ofcultivating such organisms.

In general, current photosynthetic bioreactors rely on the cultivationof microorganisms in a liquid phase system to produce biomass. Thesesystems are usually open-air pond-type reactors or enclosed tank-typereactors. Enclosed bioreactors, however, typically are considered to bean improvement over pond type reactors in many respects. Importantly,enclosed systems provide a barrier against environmental contamination.In addition, these systems allow for greater control of temperature andgas content of the liquid media.

Still, the uses of enclosed photobioreactors tend to be limited byphotosynthetic microorganisms' requirement for light (i.e., actinicradiation provides the energy required by photosynthetic microorganismsto fix carbon dioxide into organic molecules). Thus, sufficientillumination of the photosynthetic microorganisms is an unyieldingrequirement. Nevertheless, as the cell density in a liquid phasephotobioreactor increases, the ability of light to penetrate into themedia decreases, which typically limits the cell density that may beachieved. Additionally, some type of agitation of the liquid media isgenerally required to prevent unwanted sedimentation of the organisms, aprocess that requires the input of energy.

Numerous attempts have been made to devise a method of bringing light tothe organisms in liquid phase systems. For example, some systems involvecirculating the liquid culture media through transparent tubes. Otherattempts involve placing a light source within the media or introducingreflecting particles into the culture media to adjust the radiationabsorbance of the culture. Despite these efforts, a significant increasein the ability to culture organisms in liquid phase systems at highercell densities has not yet been achieved.

In addition to the aforementioned light requirement, the use of liquidphase photobioreactors has been burdened with providing thephotosynthetic microorganisms enough carbon dioxide for photosynthesis.Typically, these systems generally incorporate some type of additionalaeration system to increase the concentration of carbon dioxidedissolved in the media. Eliminating the need for aeration would greatlysimplify the system thus reducing operating costs.

Liquid phase photobioreactors also tend not to be well suited forconventional methods of continuous production. In general, thetransportation of large volumes of liquid is complex and burdensome.Further, because liquid phase systems usually require mechanisms forcirculation, agitation, aeration, and the like, it is generally simplerand more cost effective to operate only one or a few large cultivationdevices rather than numerous smaller ones. Therefore, currentlypracticed methods involve processing relatively large batches (i.e., abatch of photosynthetic microorganisms is cultivated and the entireresulting biomass is then harvested).

Thus, there is a great need in the art for advancement in photosyntheticbioreactor design. Providing a new type of photosynthetic bioreactorcapable of efficiently cultivating and harvesting relatively highdensities of photosynthetic microorganisms without large volumes ofwater or other liquid media, without the aforementioned extraordinarymeasures for supplying adequate light and carbon dioxide, and at areasonable cost would represent a substantial advance in the art, andbenefit industry and consumers alike.

SUMMARY OF THE INVENTION

Provided herein is a photobioreactor for cultivating photosyntheticmicroorganisms comprising a non-gelatinous, solid cultivation supportsuitable for providing nutrients and moisture to photosyntheticmicroorganisms and a physical barrier covering at least a portion of thesurface of the cultivation support. Devices for the large scale andcontinuous cultivation of photosynthetic microorganisms incorporatingphotobioreactors and methods of use are disclosed.

One aspect provides a photobioreactor for cultivating photosyntheticmicroorganisms. The photobioreactor comprises a non-gelatinous, solidcultivation support suitable for providing nutrients and moisture tophotosynthetic microorganisms on at least a portion of a surfacethereof, wherein said portion of the surface has a topography thatallows photosynthetic microorganisms to adhere thereto when said portionof the surface is oriented non-horizontally; and a physical barriercovering at least said portion of the surface of the cultivationsupport, wherein the physical barrier is configured so as to allowinoculation of said portion of the surface of the cultivation support,formation and maintenance of an environment suitable for the cultivationof such photosynthetic microorganisms, and harvesting of such cultivatedphotosynthetic microorganisms.

In some embodiments, the photobioreactor comprises photosyntheticmicroorganisms on said portion of the surface of the cultivationsupport. In some embodiments, the photobioreactor further comprises acell engineered to accumulate a disacharide, as described further below,wherein the cell is adhered to the solid cultivation support. In someembodiments, said portion of the surface of the cultivation support iscapable of cultivating photosynthetic microorganisms at a density of atleast about 50 grams of dry biomass per liter equivalent.

In some embodiments, the cultivation support is flexible. In someembodiments, the cultivation support comprises one or more rigidmaterials. In some embodiments, the cultivation support of thephotobioreactor comprises at least two layers, a first layer adjacent toa second layer, wherein material of the at least two layers is the samematerial or different materials. In some embodiments, the first layercomprises a high surface area growth material and the second layer apermeable type material. In some embodiments, the cultivation support ofthe photobioreactor comprises flexibly connected rigid portions, whereinthe rigid portions are comprised of the one or more rigid materials. Insome embodiments, the photobioreactor comprises a single cultivationsupport. In some embodiments, the photobioreactor comprises a pluralityof cultivation supports.

In some embodiments, the cultivation support comprises a fabric. In someembodiments, the fabric is comprised of fibers that are natural,modified natural, synthetic, or a combination thereof. In someembodiments, the fabric is a woven fabric, a knitted fabric, a felt, amesh of cross-linked fiber polymers, or a combination thereof. In someembodiments, the natural fibers are selected from the group consistingof cotton, wool, hemp, tree fiber, other cellulosic fibers, andcombinations thereof. In some embodiments, the modified natural fibersare selected from the group consisting of nitrocellulose, celluloseacetate, cellulose sulfonate, crosslinked starches, and combinationsthereof. In some embodiments, the synthetic fibers are selected from thegroup consisting of polyester, polyacrylate, polyamine, polyamide,polysulfone, and combinations thereof.

In some embodiments, the cultivation support is coated with a moistureabsorbent polymer. In some embodiments, the fabric, the fiber of thefabric, or both, are coated with a moisture absorbent polymer. In someembodiments, the moisture absorbent polymer is selected from the groupconsisting of agar, polyacrylate, polyamide, polyamine, polyethyleneglycol, modified starches, and combinations thereof.

In some embodiments, the physical barrier of the photobioreactor is atleast substantially impermeable to solid particulate and liquid but doesnot prevent the transport of gas or vapor to and from the spaceproximate to said portion of the surface of the cultivation support noractinic irradiation of said portion of the surface of the cultivationsupport. In some embodiments, the physical barrier is sufficientlyimpermeable to water vapor so that the cultivation support upon beingmoistened will retain enough of the moisture so the photosyntheticmicroorganisms remain adequately hydrated during cultivation. In someembodiments, the barrier is configured to enclose the cultivationsupport and any photosynthetic microorganisms thereon, and to bereleasably sealed during at least a portion of the cultivation of thephotosynthetic microorganisms. In some embodiments, the physical barrieris flexible. In some embodiments, the physical barrier further comprisesa first portion that is at least substantially impermeable to solidparticulate, liquid, gas, and vapor, and a second portion that ispermeable to gas and vapor but at least substantially impermeable tosolid particulate and liquid. In some embodiments, the second portion ofthe barrier has a gas or vapor exchange rate that is from at least about5 Gurley seconds to no greater than about 10,000 Gurley seconds. In someembodiments, the second portion of the barrier comprises a selectivemembrane comprising olefin fiber or polyethylene fiber material,polytetrafluoroethylene filtration media, cellulosic filter material,fiberglass filter material, polyester filter material, polyacrylatefilter material, polysulfone membranes, or nylon membranes. In someembodiments, the first portion is at least substantially transparent toactinic radiation and the second portion is not at least substantiallytransparent to actinic radiation, and the configuration of the first andsecond portions relative to each other and at least said portion of thesurface of the cultivation support is such that there a sufficientamount of actinic radiation and gas exchange to support photosynthesisby photosynthetic microorganisms.

In some embodiments, the photobioreactor further comprises a source ofactinic radiation situated between the cultivation support and thephysical barrier. In some embodiments, the physical barrier is betweenthe cultivation support and a source of actinic radiation and issufficiently transparent to such actinic radiation and sufficiently gaspermeable to allow for photosynthesis by the photosyntheticmicroorganisms during cultivation.

In some embodiments, the photobioreactor further comprises water,nutrients, or a combination thereof on, within, or on and within, thecultivation support. In some embodiments, the photobioreactor furthercomprises one or more attachment points for attaching thephotobioreactor to a structure. In some embodiments, the solidcultivation support further comprises one or more attachment points forattaching the cultivation support. In some embodiments, thephotobioreactor further comprises at least one of a fluid supply system,a nutrient supply system, a gas supply system, and a microorgansimsupply system.

In some embodiments, the photobioreactor further comprises a conveyancesystem, wherein the conveyance system moves the solid cultivationsupport so as to optimize position of the solid cultivation support forreceiving light. In some embodiments, the photobioreactor comprises aplurality of solid cultivation supports, wherein the plurality of solidcultivation supports radiate outward from a central point. In someembodiments, one or more solid cultivation supports of the plurality ofsolid cultivation supports comprises a sheet in which the depth of thesolid cultivation support is substantially less than length and width ofthe solid cultivation support. In some embodiments, the photobioreactorcomprises a conveyance system, wherein the conveyance system moves oneor more solid cultivation supports of the plurality of solid cultivationsupports so as to optimize position thereof for receiving light. In someembodiments, the conveyance system moves the plurality of solidcultivation supports around the central point so as to optimize positionof one or more solid cultivation supports for receiving light. In someembodiments, the physical barrier comprises at least a portionsufficiently transparent to actinic radiation for the cultivation ofphotosynthetic organisms and the position of the transparent portion ofthe physical barrier is movable to optimize receipt of light by thesolid cultivation support. In some embodiments, at least a portion ofthe solid cultivation support is configured so as to be exposed to anexternal source of actinic radiation. In some embodiments, thephotobioreactor comprises a source of artificial actinic radiation. Insome embodiments, the solid cultivation support comprises a materialhaving loops, such as terry cloth.

Another aspect provides a device for cultivating photosyntheticmicroorganisms. Such device comprises at least one photobioreactor asdescribed above, and a structure to which the at least onephotobioreactor is attached that orientates at least one cultivationsupport of the at least one photobioreactor non-horizontally. In someembodiments, the at least one photobioreactor is suspended from thestructure. In some embodiments, the structure is substantially coveredby the physical barrier. In some embodiments, the structure comprises aconveyor system or a component thereof such that the at least onecultivation support is capable of being conveyed along the path of theconveyor system. In some embodiments, the device further comprises one,two, or three of the following:

an inoculation station such that each cultivation support as it isconveyed along the path of the conveyor system may be inoculated withphotosynthetic microorganisms; a cultivating station such that thephotosynthetic microorganisms on each inoculated cultivation support arecultivated as each cultivation support is conveyed along the path of theconveyor system; and a harvesting station to which the cultivationsupport is conveyed so that at least a portion of the cultivatedphotosynthetic microorganisms may be harvested from each cultivationsupport. In some embodiments, the inoculation station and the harvestingstation are substantially adjacent to each other or are substantiallycoextensive. In some embodiments, the device further comprises aninducing station for inducing the synthesis of fermentable sugar byphotosynthetic microorganisms on each cultivation support. In someembodiments, the device further comprises at least one of a fluid supplysystem, a nutrient supply system, a gas supply system, or amicroorgansim supply system. In some embodiments, the device furthercomprises a photosynthetic microorganisms adhered on the solidcultivation support. In some embodiments, the device further comprises acell engineered to accumulate a disacharide, as described further below,wherein the cell is adhered to the solid cultivation support.

Other objects and features will be in part apparent and in part pointedout hereinafter.

BRIEF DESCRIPTION OF THE DRAWINGS

Those of skill in the art will understand that the drawings, describedbelow, are for illustrative purposes only. The drawings are not intendedto limit the scope of the present teachings in any way.

FIG. 1 illustrates a front view of the photobioreactor of the inventionincluding a solid cultivation support, an outer protective transparentbarrier layer, a selective panel, resealable closures, and supportelements for suspending the device.

FIG. 2 illustrates a side view of the photobioreactor of the inventionincluding a solid cultivation support, an outer protective transparentbarrier layer, a selective panel, resealable closures, and supportelements for suspending the device.

FIG. 3 illustrates an arrangement of multiple photobioreactors orcultivation supports of the invention along multiple closed loopconveyor systems radiating out from common inoculation and harvestingcenters to comprise a photobioreactor farm.

FIG. 4 is a cartoon depicting photosynthetic production of sucrose incyanobacteria.

FIG. 5 is a polypeptide sequence alignment of the Synechocystis spp. PCC6803 (Ssp6803) sucrose phosphate synthase (SPS) and sucrose phosphatephosphatase (SPP) proteins with the Synechococcus elongatus PCC 7942(Se1o7942) active SPS/SPP fusion (ASF). Ssp6803 contains separate genesencoding SPS and SPP activities. The SPS protein from Synechocystis spp.PCC 6803 bears a presumably inactive SPP domain, as many of the activesite residues are not conserved. The canonical HAD hydrolase active siteresidues are shown above the alignment with conserved amino acids shownunderlined and non-conserved residues double underlined. An eight aminoacid insertion within the inactive SPP domain of Synechocystis spp. PCC6803 SPS is italicized. Further details regarding methodology areprovided in Example 4.

FIG. 6 is schematic depiction of pLybAL11. pLybAL11 allows constructionof libraries of cyanobacterial DNA and selection for promoter sequences.The promoterless asf gene is behind bidirectional terminators, separatedby a multiple cloning site (MCS). oriV allows for plasmid replication inmost Gram-negative organisms. oriT allows for conjugal transfer of theplasmid from E. coli to a chosen cyanobacterium (or other organism) withthe assistance of the pRK2013 helper plasmid. The β-lactamase gene (bla)is present for selection in E. coli. DNA libraries can be constructed inE. coli by cloning cyanobacterial genomic DNA into the MCS. The plasmidlibrary can then be transferred to cyanobacteria by conjugation ordirect transformation. Active promoters can then be isolated byselection for resistance to chloramphenicol through expression of thechloramphenicol acetyltransferase gene (cat). The strength of thepromoters can be assessed by both assay for chloramphenicolacetyltransferase activity and direct examination of sucrose production.Further details regarding methodology are provided in Example 5.

FIG. 7 is schematic depiction of pLybAL12. pLybAL12 allows analysis ofthe capacity of preselected promoters to drive asf expression. The onlydifference between pLybAL12 and pLybAL11 is the presence of an activepromoter in front of the chloramphenicol acetyltransferase gene (cat).Specific DNA sequences isolated from cyanobacterial chromosomal DNAamplified by PCR can be cloned into the MCS. Both chloramphenicol andampicillin can be used for selection in E. coli. The plasmid library canthen be transferred to cyanobacteria by conjugation or directtransformation. Plasmid bearing cyanobacteria can then be isolated byselection for resistance to chloramphenicol through expression of thechloramphenicol acetyltransferase gene (cat). The strength of thepromoters can be assessed by both assay for chloramphenicolacetyltransferase activity and direct examination of sucrose production.Further details regarding methodology are provided in Example 5.

FIG. 8 is a cartoon depicting construction of a cyanobacterial promoterlibrary. Further details regarding methodology are provided in Example8.

FIG. 9 is a schematic diagram depicting pSMART-LCKan. Further detailsregarding methodology are provided in Example 8.

FIG. 10 is a sequence listing showing a possible promoter withinSynechococcus elongatus PCC 7942 asf. Shown is the amplified PCR productcontaining the asf gene from Synechococcus elongatus PCC 7942 that wascloned upstream of the chloramphenicol resistance marker. The regions ofasf encoding the sucrose phosphate synthase and sucrose phosphatephosphatase polypeptide activities are single underlined and doubleunderlined, respectively. All DNA sequence elements are italicized andlabeled above. Start and Stop represent the start and stop codons,respectively. SD represents the Shine-Delgarno sequence. The −35 and −10regions of the putative promoters are highlighted in gray. Furtherdetails regarding methodology are provided in Example 8.

FIG. 11 is a schematic diagram depicting a two-step protocol formarkerless deletion of genes in the cyanobacterial genome. This strategyassumes that the cyanobacterial strain being used has had its upp genedeleted. The upp gene will have been deleted during the sucrosebiosynthetic insertions. The gene of interest that has been targeted fordeletion must be identified. The starting strain is resistant to5-fluorouracil, but sensitive to kanamycin. The gene is eithercompletely or partially deleted by the insertion of a cassettecontaining a kanamycin resistance marker and an active upp, making thestrain resistant to kanamycin, but sensitive to 5-fluorouracil. The uppand kanamycin resistance markers can then be removed, making the strainonce again resistant to 5-fluorouracil, but sensitive to kanamycin.Further details regarding methodology are provided in Example 12.

FIG. 12 is a schematic diagram of a photobioreactor embodiment. FIG. 12Aprovides a front view while FIG. 12B provides a side view. Thephotobioreactor includes suspension element (6); culture media supply(8); gas supply (10); growth surface (2); outer barrier layer (7); quickconnector; and product harvest line (9).

FIG. 13 is a schematic diagram of a growth surface in a single materialformat (FIG. 13A) and a hybrid material format (FIG. 13B).

DETAILED DESCRIPTION OF THE INVENTION

The present application relates to fermentable sugar accumulatingphotosynthetic microorganisms, solid-phase photoreactor devices, andmethods of using each.

In the fermentable sugar accumulating photosynthetic microorganisms, itmay be preferable to produce a dissaccharide sugar not generallyutilized by the photosynthetic microorganisms, which therefore canaccumulate within the cultivated biomass (e.g., sucrose, trehalose). Insome embodiments, photosynthetic microorganisms are geneticallyengineered to synthesize a dissaccharide sugar normally producedaccording to osmotic stress pathways (e.g., sucrose or trehalose) suchthat the sugar is produced in the absence of, or at reduced levels of,osmotic stress. Because of the greater efficiency and lowerenvironmental impact of growing photosynthetic microorganisms comparedto higher plants, the method represents important improvements insustainability over current biofuel production practices.Advantageously, the foregoing method of synthesizing a dissaccharidesugar has been adapted to occur within the photobioreactor(s) of thepresent invention.

The photobioreactor described herein utilizes a solid cultivationsupport. Advantageously, the difficulty of providing adequate lightexposures is alleviated, at least in part. Utilizing the aforementionedsolid cultivation support in a photobioreactor can allow for cultivationand growth of photosynthetic microorganisms at cell densities greaterthan those of commercial-scale liquid phase bioreactors (e.g., celldensities in excess of 200 grams of dry biomass per liter equivalent).In addition, various embodiments of the photobioreactor described hereincan be operated using less energy and more simply than conventionalcommercial-scale liquid phase photobioreactors.

Embodiments of the photobioreactor described herein provide additionalbenefits over conventional liquid phase photobioreactors. For example,liquid systems typically require special equipment to deliver adequateconcentrations/amount of carbon dioxide to the photosyntheticmicroorganisms to support their growth and photosynthesis. In contrast,by growing the microorganisms on a solid cultivation support, carbondioxide can be provided in a relatively simple, less costly manner, suchas exposure to surrounding air. If additional carbon dioxide is desired,it can easily be delivered by, for example, adding it to the atmosphere(e.g., air) surrounding or in contact with the cultivation support.Another benefit is ease of transport. Liquid phase photobioreactors canbe a pond (completely immobile) or bulky tanks or collections of tubing.In contrast, in various embodiments, the photobioreactor is flat andflexible, which allows for it or a multiplicity of them to be stacked,rolled up, folded, and/or configured in a similar manner for relativelyeasy transport. In various embodiments, the photobioreactor can beconfigured in a manner such that it is suspended from a system thatallows for easy conveyance of one or more photobioreactors from onelocation to another. This portability may be utilized on a commercialscale to allow for efficient methods of handling and processing largenumbers of photobioreactors in a continuous-type manner.

One aspect of the application is directed to a method of fermentablesugar feedstock production by photosynthetic microorganisms. Preferably,the fermentable sugar is a fermentable disaccharide sugar. Examples offermentable disaccharide sugars include, but are not limited to sucroseand trehalose. The fermentable sugar can be a disaccharide not generallyutilized by photosynthetic microorganisms. For example, trehalose is notgenerally utilized by cyanobacteria and therefore can accumulate withinthe cultivated biomass without substantial degradation by endogenousmetabolic pathways. The fermentable sugar can be a disaccharide that isgenerally utilized by photosynthetic microorganisms. For a disaccharidenot used as a primary energy source, the disaccharide can often beaccumulated to sufficient levels even in the presence of endogenousmetabolic pathways. Where endogenous degradation pathways specific forthe target fermentable sugar, the photosynthetic microorganism can beengineered to reduce or eliminate such activity. For example, acyanobacterium engineered to accumulate sucrose can be furtherengineered to reduce or eliminate sucrose invertase activity. In variousembodiments, strains of photosynthetic microorganisms that synthesizefermentable disaccharide sugar in response to osmotic or matric waterstress can be used. In other embodiments transgenic strains ofphotosynthetic microorganisms engineered to accumulate fermentabledisaccharide sugar in the absence of, or reduced levels of, osmoticstress. Advantageously, the foregoing methods of synthesizingfermentable disaccharide sugar can be adapted to occur withinphotobioreactors described herein.

Because of the greater efficiency and lower environmental impact ofgrowing photosynthetic microorganisms compared to higher plants,compositions, devices, and methods described herein represent importantimprovements in sustainability over current biofuel productionpractices.

Photosynthetic Microorganism

Provided herein is a photosynthetic microorganism genetically engineeredto accumulate a dissaccharide sugar. The photosynthetic microorganismcan be, for example, a naturally photosynthetic microorganism, such as acyanobacterium, or an engineered photosynthetic microorganism, such asan artificially photosynthetic bacterium. Examples of the accumulateddissaccharide sugar include, but are not limited to sucrose, trehalose,gluocosylglycerol, and mannosylfructose. In various embodiments, one ormore genes encoding the protein(s) responsible for producing the desireddissaccharide from corresponding phosphorylated monomers is engineeredin a host photosynthetic microorganism (e.g., cyanobacterium) so as toresult in the accumulation of the desired dissaccharide. In someembodiments, an endogenous pathway of the host photosyntheticmicroorganism is engineered so as to accumulate a dissaccharide sugar.For example, the osmotic sucrose pathway in cyanobacteria can beengineered to accumulate sucrose in the absence of osmotic stress. Insome embodiments, an exogenous dissaccharide pathway is engineered incyanobacteria so as to accumulate a dissaccharide sugar. For example,the osmotic trehalose pathway from E. coli can be engineered toaccumulate trehalose in cyanobacteria.

Synthase and Phosphotase

A photosynthetic microorganism can be transformed so as to have asynthase activity and a phosphotase activity for the desireddissaccharide. For example, a cyanobacterium can be engineered to havesucrose phosphate synthase activity and sucrose phosphate phosphataseactivity. As another example, a cyanobacterium can be engineered to havetrehalose phosphate synthase activity and trehalose phosphatephosphatase activity. As another example, a cyanobacterium can beengineered to have gluocosylglycerol phosphate synthase activity andgluocosylglycerol phosphate phosphatase activity. As another example, acyanobacterium can be engineered to have mannosylfructose phosphatesynthase activity and mannosylfructose phosphate phosphatase activity.It is contemplated these activities can likewise be engineered in otherphotosynthetic microorganisms.

Synthase activity and phosphotase activity can be engineered into aphotosynthetic microorganism by way of the individual genes, oneencoding a polypeptide having synthase activity and the other encoding apolypeptide having phosphatase activity; or by one gene encoding bothsynthase activity and phosphatase activity. For example, synthaseactivity and phosphatase activity can be present in a fusionpolypeptide.

The monomeric sugars of the desired dissaccharide can be endogenous orexogenous to the photosynthetic microorganism. Where monomeric sugars ofthe desired dissaccharide are endogenous, the photosyntheticmicroorganism can be engineered to produce increased levels of suchmonomers. Where monomeric sugars of the desired dissaccharide areexogenous, the photosynthetic microorganism can be engineered to producesuch exogenous monomers.

The photosynthetic microorganism can be engineered to synthesize andaccumulate the desired dissaccharide continuously, after somedevelopmental state, or upon being induced to do so. Induction ofdissaccharide synthesis can be according to the actions of an induciblepromoter associated with the encoded synthase or phosphotase and aninducing agent, as discussed in further detail herein.

In some embodiments, transformed cyanobacteria, as described herein, canaccumulate at least about 0.1 micrograms of a dissaccharide (e.g.,sucrose, trehalose, glucosylglycerol, or mannosylfructose) per minuteper gram dry biomass. In some embodiments, transformed cyanobacteria canaccumulate at least about 0.1 up to about 10 micrograms of adissaccharide (e.g., sucrose, trehalose, glucosylglycerol, ormannosylfructose) per minute per gram dry biomass. For example,transformed cyanobacteria can accumulate at least about 0.2, at leastabout 0.3, at least about 0.4, at least about 0.5, at least about 0.6,at least about 0.7, at least about 0.8, or at least about 0.9 microgramsof a dissaccharide (e.g., sucrose, trehalose, glucosylglycerol, ormannosylfructose) per minute per gram dry biomass. In other embodiments,various transformed photosynthetic microorganisms accumulate similaramounts of a dissaccharide.

It is contemplated that that various embodiments will accumulate adisaccharide (e.g., sucrose, trehalose, glucosylglycerol, ormannosylfructose) at defined ranges of the values above. For example,some transformed cyanobacteria can accumulate at least about 0.1 up toabout 0.9 micrograms of a disaccharide (e.g., sucrose, trehalose,glucosylglycerol, or mannosylfructose) per minute per gram dry biomass;at least about 0.1 up to about 0.8 micrograms of a disaccharide (e.g.,sucrose, trehalose, glucosylglycerol, or mannosylfructose) per minuteper gram dry biomass; at least about 0.1 up to about 0.7 micrograms of adisaccharide (e.g., sucrose, trehalose, glucosylglycerol, ormannosylfructose) per minute per gram dry biomass; etc. Similarly, sometransformed cyanobacteria can accumulate at least about 0.2 up to about1.0 micrograms of a disaccharide (e.g., sucrose, trehalose,glucosylglycerol, or mannosylfructose) per minute per gram dry biomass;at least about 0.3 up to about 1.0 micrograms of a disaccharide (e.g.,sucrose, trehalose, glucosylglycerol, or mannosylfructose) per minuteper gram dry biomass; at least about 0.4 up to about 1.0 micrograms of adisaccharide (e.g., sucrose, trehalose, glucosylglycerol, ormannosylfructose) per minute per gram dry biomass; at least about 0.5 upto about 1.0 micrograms of a disaccharide (e.g., sucrose, trehalose,glucosylglycerol, or mannosylfructose) per minute per gram dry biomass;at least about 0.6 up to about 1.0 micrograms of a disaccharide (e.g.,sucrose, trehalose, glucosylglycerol, or mannosylfructose) per minuteper gram dry biomass; at least about 0.7 up to about 1.0 micrograms of adisaccharide (e.g., sucrose, trehalose, glucosylglycerol, ormannosylfructose) per minute per gram dry biomass; at least about 0.8 upto about 1.0 micrograms of a disaccharide (e.g., sucrose, trehalose,glucosylglycerol, or mannosylfructose) per minute per gram dry biomass;or at least about 0.9 up to about 1.0 micrograms of a disaccharide(e.g., sucrose, trehalose, glucosylglycerol, or mannosylfructose) perminute per gram dry biomass. Methods for assaying sugar accumulation ishost cells are well-known to those of skill in the art (see e.g.,Example 10).

Host

The host genetically engineered to accumulate a dissaccharide sugar canbe any photosynthetic microorganism. The photosynthetic microorganismcan be, for example, a naturally photosynthetic microorganism, such as acyanobacterium, or an engineered photosynthetic microorganism, such asan artificially photosynthetic bacterium. Exemplary microorgansims thatare either naturally photosynthetic or can be engineered to bephotosynthetic include, but are not limited to, bacteria; fungi;archaea; protists; microscopic plants, such as a green algae; andanimals such as plankton, planarian, and amoeba. Examples of naturallyoccurring photosynthetic microorganisms include, but are not limited to,Spirulina maximum, Spirulina platensis, Dunaliella salina, Botrycoccusbraunii, Chlorella vulgaris, Chlorella pyrenoidosa, Serenastrumcapricomutum, Scenedesmus auadricauda, Porphyridium cruentum,Scenedesmus acutus, Dunaliella sp., Scenedesmus obliquus, Anabaenopsis,Aulosira, Cylindrospermum, Synechoccus sp., Synechocystis sp., and/orTolypothrix.

Preferably, the host photosynthetic microorganism is a cyanobacterium.Cyanobacteria, also known as blue-green algae, are a broad range ofoxygengenic photoautotophs. The host cyanobacterium can be anyphotosynthetic microorganism from the phylum Cyanophyta. The hostcyanobacterium can have a unicellular or colonial (e.g., filaments,sheets, or balls) morphology. Preferably, the host cyanobacterium is aunicellular cyanobacterium. Examples of cyanobacteria that can beengineered to accumulate a disaccharide sugar include, but are notlimited to, the genus Synechocystis, Synechococcus, Thermosynechococcus,Nostoc, Prochlorococcu, Microcystis, Anabaena, Spirulina, andGloeobacter. Preferably the host cyanobacterium is a Synechocystis spp.or Synechococcus spp. More preferably, the host cyanobacterium isSynechococcus elongatus PCC 7942 (ATCC 33912) and/or Synechocystis spp.PCC 6803 (ATCC 27184).

Sucrose

Biosynthesis of sucrose in a photosynthetic microorganism, such ascyanobacteria, can be accomplished through the catalytic action of twoenzyme activities, sucrose phosphate synthase (sps) and sucrosephosphate phosphatase (spp), functioning in sequence (see e.g., FIG. 4).Such activities are present in some cyanobacteria for acclimation toosmotic and matric water stress (see e.g., Lunn, J. E. 2002. PlantPhysiol 128, 1490-1500). Either or both of these activities can beengineered in a cyanobacterium so as to result in accumulation ofsucrose.

A gene of particular interest for engineering a photosyntheticmicroorganism to accumulate sucrose is the active sps/spp fusion (asf)gene from Synechococcus elongatus PCC 7942. Asf has both sps and sppbiosynthetic functions (see e.g., Example 4). In some embodiments, anASF-encoding nucleotide sequence is cloned from its native source (e.g.,Synechococcus elongatus PCC 7942) and inserted into a hostcyanobacterium (see e.g., Examples 4-9). In some embodiments, atransformed host photosynthetic microorganism comprises an asfpolynucleotide of SEQ ID NO: 1. In some embodiments, a photosyntheticmicroorganism is transformed with a nucleotide sequence encoding ASFpolypeptide of SEQ ID NO: 2. In further embodiments, a transformed hostphotosynthetic microorganism comprises a nucleotide sequence having atleast about 80% sequence identity to SEQ ID NO: 1 or a nucleotidesequence encoding a polypeptide having sps and spp activity and at leastabout 80% sequence identity to SEQ ID NO: 2. As an example, atransformed host photosynthetic microorganism, such as a cyanobacterium,can comprise a nucleotide sequence having at least about 85%, at leastabout 90%, at least about 95%, or at least about 99% sequence identityto SEQ ID NO: 1, wherein the transformed host exhibits ASF, SPS, and/orSPP activity and/or accumulation of sucrose. As an example, atransformed host photosynthetic microorganism can comprise a nucleotidesequence encoding a polypeptide having at least about 85%, at leastabout 90%, at least about 95%, or at least about 99% sequence identityto SEQ ID NO: 2, wherein the transformed host exhibits ASF, SPS, and/orSPP activity and/or accumulation of sucrose. As another example, atransformed host photosynthetic microorganism can comprise a nucleotidesequence that hybridizes under stringent conditions to SEQ ID NO: 1 overthe entire length of SEQ ID NO: 1, and which encodes an active SPS/SPPfusion (ASF) polypeptide. As a further example, a transformed hostphotosynthetic microorganism can comprise the complement to any of theabove sequences.

In some embodiments, a sucrose phosphate synthase (sps) (see e.g., SEQID NO: 3 encoding sps gene and SEQ ID NO: 4 encoding SPS polypeptide),or homologue thereof, is engineered to be expressed or overexpressed ina transformed photosynthetic microorganism. For example, aphotosynthetic microorganism can be transformed with a nucleotide havinga sequence of SEQ ID NO: 3 so as to express sucrose phosphate synthase.As another example, a photosynthetic microorganism can be transformedwith a nucleotide having at least about 80%, at least about 85%, atleast about 90%, at least about 95%, or at least about 99% percentidentity to SEQ ID NO: 3 encoding a polypeptide having sucrose phosphatesynthase. As another example, a transformed host photosyntheticmicroorganism can comprise a nucleotide sequence encoding a polypeptidehaving at least about 85%, at least about 90%, at least about 95%, or atleast about 99% sequence identity to SEQ ID NO: 4, wherein thetransformed host exhibits SPS activity and/or accumulation of sucrose.

In some embodiments, sucrose phosphate phosphatase (spp) (see e.g., SEQID NO: 5 encoding spp gene and SEQ ID NO: 6 encoding SPP polypeptide),or homologue thereof, is engineered to be expressed or overexpressed ina transformed photosynthetic microorganism. For example, aphotosynthetic microorganism, such as a cyanobacterium, can betransformed with a nucleotide having a sequence of SEQ ID NO: 5 so as toexpress sucrose phosphate phosphatase. As another example, aphotosynthetic microorganism can be transformed with a nucleotide havingat least about 80%, at least about 85%, at least about 90%, at leastabout 95%, or at least about 99% percent identity to SEQ ID NO: 5encoding a polypeptide having sucrose phosphate phosphatase activity. Asanother example, a transformed host photosynthetic microorganism cancomprise a nucleotide sequence encoding a polypeptide having at leastabout 85%, at least about 90%, at least about 95%, or at least about 99%sequence identity to SEQ ID NO: 6, wherein the transformed host exhibitsSPP activity and/or accumulation of sucrose.

In some embodiments, a photosynthetic microorganism is engineered toexpress one or more of ASF, SPS, and/or SPP. For example, aphotosynthetic microorganism, such as a cyanobacterium, can beengineered to express ASF and SPS; ASF and SPP; SPS and SPP; or ASF,SPS, and SPP.

Trehalose

Biosynthesis of trehalose can be accomplished through the catalyticaction of two enzyme activities, trehalose phosphate synthase (tps) andtrehalose phosphate phosphatase (tpp), functioning in sequence. Eitheror both of these activities can be engineered in a photosyntheticmicroorganism so as to result in accumulation of trehalose. Biosynthesisof trehalose does not naturally occur in some photosyntheticmicroorganisms, such as cyanobacteria.

In some embodiments, a trehalose phosphate synthase (tps) (see e.g., SEQID NO: 76 encoding tps gene and SEQ ID NO: 77 encoding TPS polypeptide),or homologue thereof, is engineered to be expressed or overexpressed ina transformed photosynthetic microorganism. For example, aphotosynthetic microorganism, such as cyanobacterium, can be transformedwith a nucleotide having a sequence of SEQ ID NO: 76 so as to expresstrehalose phosphate synthase. As another example, a photosyntheticmicroorganism can be transformed with a nucleotide having at least about80%, at least about 85%, at least about 90%, at least about 95%, or atleast about 99% percent identity to SEQ ID NO: 76 encoding a polypeptidehaving trehalose phosphate synthase. As another example, a transformedhost photosynthetic microorganism can comprise a nucleotide sequenceencoding a polypeptide having at least about 85%, at least about 90%, atleast about 95%, or at least about 99% sequence identity to SEQ ID NO:77, wherein the transformed host exhibits TPS activity and/oraccumulation of trehalose.

In some embodiments, trehalose phosphate phosphatase (tpp) (see e.g.,SEQ ID NO: 78 encoding tpp gene and SEQ ID NO: 79 encoding TPPpolypeptide), or homologue thereof, is engineered to be expressed oroverexpressed in a transformed photosynthetic microorganism. Forexample, a photosynthetic microorganism, such as a cyanobacterium, canbe transformed with a nucleotide having a sequence of SEQ ID NO: 78 soas to express trehalose phosphate phosphatase. As another example, aphotosynthetic microorganism can be transformed with a nucleotide havingat least about 80%, at least about 85%, at least about 90%, at leastabout 95%, or at least about 99% percent identity to SEQ ID NO: 78encoding a polypeptide having trehalose phosphate phosphatase activity.As another example, a transformed host photosynthetic microorganism cancomprise a nucleotide sequence encoding a polypeptide having at leastabout 85%, at least about 90%, at least about 95%, or at least about 99%sequence identity to SEQ ID NO: 79, wherein the transformed hostexhibits TPP activity and/or accumulation of trehalose.

Glucosylglycerol

In some embodiments, a glucosylglycerolphosphate synthase (gps) (seee.g., SEQ ID NO: 80 encoding gps gene and SEQ ID NO: 81 encoding GPSpolypeptide), or homologue thereof, is engineered to be expressed oroverexpressed in a transformed photosynthetic microorganism. Forexample, a photosynthetic microorganism, such as a cyanobacterium, canbe transformed with a nucleotide having a sequence of SEQ ID NO: 80 soas to express glucosylglycerolphosphate synthase. As another example, aphotosynthetic microorganism can be transformed with a nucleotide havingat least about 80%, at least about 85%, at least about 90%, at leastabout 95%, or at least about 99% percent identity to SEQ ID NO: 80encoding a polypeptide having glucosylglycerolphosphate synthase. Asanother example, a transformed host photosynthetic microorganism cancomprise a nucleotide sequence encoding a polypeptide having at leastabout 85%, at least about 90%, at least about 95%, or at least about 99%sequence identity to SEQ ID NO: 81, wherein the transformed hostexhibits GPS activity and/or accumulation of glucosylgycerol.

In some embodiments, glucosylglycerolphosphate phosphatase (gpp) (seee.g., SEQ ID NO: 82 encoding gpp gene and SEQ ID NO: 83 encoding GPPpolypeptide), or homologue thereof, is engineered to be expressed oroverexpressed in a transformed photosynthetic microorganism. Forexample, a photosynthetic microorganism, such as a cyanobacterium, canbe transformed with a nucleotide having a sequence of SEQ ID NO: 82 soas to express glucosylglycerolphosphate phosphatase. As another example,a photosynthetic microorganism can be transformed with a nucleotidehaving at least about 80%, at least about 85%, at least about 90%, atleast about 95%, or at least about 99% percent identity to SEQ ID NO: 82encoding a polypeptide having glucosylglycerolphosphate phosphataseactivity. As another example, a transformed host photosyntheticmicroorganism can comprise a nucleotide sequence encoding a polypeptidehaving at least about 85%, at least about 90%, at least about 95%, or atleast about 99% sequence identity to SEQ ID NO: 83, wherein thetransformed host exhibits GPP activity and/or accumulation ofglucosylgycerol.

Mannosylfructose

In some embodiments, a mannosylfructose phosphate synthase (mps) (seee.g., SEQ ID NO: 84 encoding mps gene and SEQ ID NO: 85 encoding MPSpolypeptide), or homologue thereof, is engineered to be expressed oroverexpressed in a transformed photosynthetic microorganism. Forexample, a photosynthetic microorganism, such as a cyanobacterium, canbe transformed with a nucleotide having a sequence of SEQ ID NO: 84 soas to express mannosylfructose phosphate synthase. As another example, aphotosynthetic microorganism can be transformed with a nucleotide havingat least about 80%, at least about 85%, at least about 90%, at leastabout 95%, or at least about 99% percent identity to SEQ ID NO: 84encoding a polypeptide having mannosylfructose phosphate synthase. Asanother example, a transformed host photosynthetic microorganism cancomprise a nucleotide sequence encoding a polypeptide having at leastabout 85%, at least about 90%, at least about 95%, or at least about 99%sequence identity to SEQ ID NO: 85, wherein the transformed hostexhibits MPS activity and/or accumulation of mannosylfructose.

In some embodiments, mannosylfructose phosphate phosphatase (mpp) (seee.g., SEQ ID NO: 86 encoding mpp gene and SEQ ID NO: 87 encoding MPPpolypeptide), or homologue thereof, is engineered to be expressed oroverexpressed in a transformed photosynthetic microorganism. Forexample, a photosynthetic microorganism, such as a cyanobacterium, canbe transformed with a nucleotide having a sequence of SEQ ID NO: 86 soas to express mannosylfructose phosphate phosphatase. As anotherexample, a photosynthetic microorganism can be transformed with anucleotide having at least about 80%, at least about 85%, at least about90%, at least about 95%, or at least about 99% percent identity to SEQID NO: 86 encoding a polypeptide having mannosylfructose phosphatephosphatase activity. As another example, a transformed hostphotosynthetic microorganism can comprise a nucleotide sequence encodinga polypeptide having at least about 85%, at least about 90%, at leastabout 95%, or at least about 99% sequence identity to SEQ ID NO: 87,wherein the transformed host exhibits MPP activity and/or accumulationof mannosylfructose.

Molecular Engineering

Design, generation, and testing of the variant nucleotides, and theirencoded polypeptides, having the above required percent identities to anasf sequence and retaining a required activity of the expressed proteinand/or sugar accumulation phenotype is within the skill of the art. Forexample, directed evolution and rapid isolation of mutants can beaccording to methods described in references including, but not limitedto, Link et al. (2007) Nature Reviews 5(9), 680-688; Sanger et al.(1991)

Gene 97(1), 119-123; Ghadessy et al. (2001) Proc Natl Acad Sci USA 98(8)4552-4557. Thus, one skilled in the art could generate a large number ofnucleotide (e.g., asf, sps, spp, tps, tpp, gps, gpp, mps, or mpp) and/orpolypeptide (e.g., ASF, SPS, SPP, TPS, TPP, GPS, GPP, MPS, or MPP)variants having, for example, at least 95-99% identity to the referencesequence described herein and screen such for phenotypes includingdisaccharide accumulation according to methods routine in the art.Generally, conservative substitutions can be made at any position solong as the required activity is retained.

Nucleotide and/or amino acid sequence identity percent (%) is understoodas the percentage of nucleotide or amino acid residues that areidentical with nucleotide or amino acid residues in a candidate sequencein comparison to a reference sequence when the two sequences arealigned. To determine percent identity, sequences are aligned and ifnecessary, gaps are introduced to achieve the maximum percent sequenceidentity. Sequence alignment procedures to determine percent identityare well known to those of skill in the art. Often publicly availablecomputer software such as BLAST, BLAST2, ALIGN2 or Megalign (DNASTAR)software is used to align sequences. Those skilled in the art candetermine appropriate parameters for measuring alignment, including anyalgorithms needed to achieve maximal alignment over the full-length ofthe sequences being compared. When sequences are aligned, the percentsequence identity of a given sequence A to, with, or against a givensequence B (which can alternatively be phrased as a given sequence Athat has or comprises a certain percent sequence identity to, with, oragainst a given sequence B) can be calculated as: percent sequenceidentity=X/Y100, where X is the number of residues scored as identicalmatches by the sequence alignment program's or algorithm's alignment ofA and B and Y is the total number of residues in B. If the length ofsequence A is not equal to the length of sequence B, the percentsequence identity of A to B will not equal the percent sequence identityof B to A.

“Highly stringent hybridization conditions” are defined as hybridizationat 65° C. in a 6×SSC buffer (i.e., 0.9 M sodium chloride and 0.09 Msodium citrate). Given these conditions, a determination can be made asto whether a given set of sequences will hybridize by calculating themelting temperature (T_(m)) of a DNA duplex between the two sequences.If a particular duplex has a melting temperature lower than 65° C. inthe salt conditions of a 6×SSC, then the two sequences will nothybridize. On the other hand, if the melting temperature is above 65° C.in the same salt conditions, then the sequences will hybridize. Ingeneral, the melting temperature for any hybridized DNA:DNA sequence canbe determined using the following formula: T_(m)=81.5°C.+16.6(log₁₀[Na⁺])+0.41(fraction G/C content)−0.63(%formamide)−(600/1). Furthermore, the T_(m) of a DNA:DNA hybrid isdecreased by 1-1.5° C. for every 1% decrease in nucleotide identity (seee.g., Sambrook and Russel, 2006).

Host cells can be transformed using a variety of standard techniquesknown to the art (see, e.g., Sambrook and Russel (2006) CondensedProtocols from Molecular Cloning: A Laboratory Manual, Cold SpringHarbor Laboratory Press, ISBN-10: 0879697717; Ausubel et al. (2002)Short Protocols in Molecular Biology, 5th ed., Current Protocols,ISBN-10: 0471250929; Sambrook and Russel (2001) Molecular Cloning: ALaboratory Manual, 3d ed., Cold Spring Harbor Laboratory Press, ISBN-10:0879695773; Elhai, J. and Wolk, C. P. 1988. Methods in Enzymology 167,747-754). Such techniques include, but are not limited to, viralinfection, calcium phosphate transfection, liposome-mediatedtransfection, microprojectile-mediated delivery, receptor-mediateduptake, cell fusion, electroporation, and the like. The transfectedcells can be selected and propagated to provide recombinant host cellsthat comprise the expression vector stably integrated in the host cellgenome.

Promoter

One or more of the nucleotide sequences discussed above (e.g., asf, sps,spp, tps, tpp, mps, mpp, gps, gpp) can be operably linked to a promoterthat can function in the host photosynthetic microorganism. Where thehost is cyanobacteria, preferably, the promoter can function efficientlyin both cyanobacteria and a bacteria, such as E. coli. Promoterselection can allow expression of a desired gene product under a varietyof conditions.

Promoters can be selected for optimal function in a photosyntheticmicroorganism host cell, such as a cyanobacterium, into which the vectorconstruct will be inserted. Promoters can also be selected on the basisof their regulatory features. Examples of such features includeenhancement of transcriptional activity and inducibility.

The promoter can be an inducible promoter. For example, the promoter canbe induced according to temperature, pH, a hormone, a metabolite (e.g.,lactose, mannitol, an amino acid), light (e.g., wavelength specific),osmotic potential (e.g., salt induced), a heavy metal, or an antibiotic.Numerous standard inducible promoters will be known to one of skill inthe art.

In some embodiments, the promoter is a temperature inducible promoter.For example, the Lambda promoter is a temperature inducible promoterthat can function in cyanobacteria. Surprisingly, the Lambda promoterfunctions at a temperature different than when utilized in E. coli. InE. coli, the Lambda promoter is most active at 42° C., a temperatureabove the normal viability range for cyanobacteria. Generally, in E.coli, the Lambda promoter has about a 5% to 10% increased expressionfrom about 30° C. to 35° C. and at about 37° C. has about a 20%increased expression; but from about 37° C. to 42° C. provides about100% increased expression. In cyanobacteria, the Lambda promoter is mostactive at around 30° C. to 35° C., an ideal growth temperature range forcyanobacteria and a range much lower than optimal expression of theLambda promoter in E. coli. So, the Lambda promoter provides foreffective expression of disaccharide biotsynthetic activity incyanobacteria.

Examples of promoters that can be inserted into the plasmid include, butare not limited to, carB, nirA, psbAII, dnaK, kaiA, and λ_(PR) (seee.g., Example 6). In some embodiments, the promoter can functionefficiently in both cyanobacteria and E. coli. In some embodiments, theasf coding region comprises a promoter with said coding region (seee.g., Example 8). For example, the asf coding region can comprise apromoter in front of the SPP domain of asf (see e.g., FIG. 10). Such aninternal promoter can occur with or without a promoter at the start ofthe asf coding region.

The term “chimeric” is understood to refer to the product of the fusionof portions of two or more different polynucleotide molecules. “Chimericpromoter” is understood to refer to a promoter produced through themanipulation of known promoters or other polynucleotide molecules. Suchchimeric promoters can combine enhancer domains that can confer ormodulate gene expression from one or more promoters or regulatoryelements, for example, by fusing a heterologous enhancer domain from afirst promoter to a second promoter with its own partial or completeregulatory elements. Thus, the design, construction, and use of chimericpromoters according to the methods disclosed herein for modulating theexpression of operably linked polynucleotide sequences are encompassedby the present invention.

Novel chimeric promoters can be designed or engineered by a number ofmethods. For example, a chimeric promoter may be produced by fusing anenhancer domain from a first promoter to a second promoter. Theresultant chimeric promoter may have novel expression propertiesrelative to the first or second promoters. Novel chimeric promoters canbe constructed such that the enhancer domain from a first promoter isfused at the 5′ end, at the 3′ end, or at any position internal to thesecond promoter.

Constructs

Any of the transcribable polynucleotide molecule sequences describedabove can be provided in a construct. Constructs of the presentinvention generally include a promoter functional in the hostphotosynthetic microorganism, such as cyanobacteria, operably linked toa transcribable polynucleotide molecule for disaccharide biosynthesis(e.g., asf, sps, spp, tps, tpp, mps, mpp, gps, gpp), such as provided inSEQ ID NO: 1, 3, 5, 76, 78, 80, 82, 84, and 86, and variants thereof asdiscussed above.

Exemplary promoters are discussed above. One or more additionalpromoters may also be provided in the recombinant construct. Thesepromoters can be operably linked to any of the transcribablepolynucleotide molecule sequences described above.

The term “construct” is understood to refer to any recombinantpolynucleotide molecule such as a plasmid, cosmid, virus, autonomouslyreplicating polynucleotide molecule, phage, or linear or circularsingle-stranded or double-stranded DNA or RNA polynucleotide molecule,derived from any source, capable of genomic integration or autonomousreplication, comprising a polynucleotide molecule where one or morepolynucleotide molecule has been linked in a functionally operativemanner, i.e. operably linked. The term “vector” or “vector construct” isunderstood to refer to any recombinant polynucleotide construct that maybe used for the purpose of transformation, i.e., the introduction ofheterologous DNA into a host photosynthetic microorganism, such as acyanobacterium.

In addition, constructs may include, but are not limited to, additionalpolynucleotide molecules from an untranslated region of the gene ofinterest. These additional polynucleotide molecules can be derived froma source that is native or heterologous with respect to the otherelements present in the construct.

Plasmid

In some embodiments, a host photosynthetic microorgansim, such as acyanobacterium, is transformed with a plasmid-based expression system(see e.g., Example 5). Preferably the plasmid encoding the gene ofinterest comprises a promoter, such as one or more of those discussedabove. For plasmid based transformation, preferred is a broad host rangeplasmid that enables function in both E. coli and cyanobacteria, whichprovides the advantage of working in a convenient fast growing wellunderstood system (E. coli) that can be efficiently transferred to thefinal host (cyanobacteria). In some embodiments, plasmid basedtransformation and chromosomal integration are used in conjunction,where the plasmid protocol is used for design and testing of genevariants followed by chromosomal integration of identified variants.

Host strains developed according to the approaches described herein canbe evaluated by a number of means known in the art (see e.g., Studier(2005) Protein Expr Purif. 41(1), 207-234; Gellissen, ed. (2005)Production of Recombinant Proteins: Novel Microbial and EukaryoticExpression Systems, Wiley-VCH, ISBN-10: 3527310363; Baneyx (2004)Protein Expression Technologies, Taylor & Francis, ISBN-10: 0954523253).

Provided herein are nucleotide sequences for plasmid constructs encodingsps, spp, and/or asf. Examples of plasmid constructs encoding sps, spp,and/or asf include, but are not limited to, pLybAL11 (SEQ ID NO: 19)(see e.g., FIG. 6) and pLybAL12 (SEQ ID NO: 20) (see e.g., FIG. 7). Alsoprovided herein are nucleotide sequences for plasmid constructs encodingtps and tpp. Examples of plasmid constructs encoding tps and tppinclude, but are not limited to, pLybAL23 (SEQ ID NO: 118). A skilledartisan will understand that similar constructs can be generated forbiosynthetic genes necessary for accumulation of other disaccharides,such as glucosylglycerol and mannosylfructose.

In some embodiments, the transformed host photosynthetic microorganismcomprises pLybAL11 (SEQ ID NO: 19) or pLybAL12 (SEQ ID NO: 20). In someembodiments, the transformed host photosynthetic microorganism comprisespLybAL23 (SEQ ID NO: 118). For example, a transformed cyanobacterium cancomprise pLybAL11 (SEQ ID NO: 19), pLybAL12 (SEQ ID NO: 20), or pLybAL23(SEQ ID NO: 118).

A plasmid construct comprising a disaccharide biosynthetic gene(s) canalso include a promoter. Examples of plasmid constructs comprising sps,spp, and/or asf and a promoter include, but are not limited to, pLybAL7f(SEQ ID NO: 65); pLybAL8f, including kanamycin resistance (SEQ ID NO:69); pLybAL13f (SEQ ID NO: 51), pLyAL13r (SEQ ID NO: 52), pLybAL14f (SEQID NO: 53), pLybAL14r (SEQ ID NO: 54), pLybAL15 (SEQ ID NO: 44),pLybAL16 (SEQ ID NO: 45), pLybAL17 (SEQ ID NO: 46), pLybAL18 (SEQ ID NO:47), pLybAL19 (SEQ ID NO: 48), pLybAL21 (SEQ ID NO: 49), and pLybAL22(SEQ ID NO: 50). Examples of plasmid constructs comprising tps and tppand a promoter include, but are not limited to, pLybAL23 (SEQ ID NO:118), pLybAL28 (SEQ ID NO: 121), pLybAL29 (SEQ ID NO: 122), and pLybAL30(SEQ ID NO: 123). A skilled artisan will understand that similarpromoter containing constructs can be generated for biosynthetic genesnecessary for accumulation of other disaccharides, such asglucosylglycerol and mannosylfructose.

In some embodiments, the transformed host cyanobacterium comprisespLybAL7f (SEQ ID NO: 65); pLybAL8f (SEQ ID NO: 69); pLybAL13f (SEQ IDNO: 51), pLyAL13r (SEQ ID NO: 52), pLybAL14f (SEQ ID NO: 53), pLybAL14r(SEQ ID NO: 54), pLybAL15 (SEQ ID NO: 44), pLybAL16 (SEQ ID NO: 45),pLybAL17 (SEQ ID NO: 46), pLybAL18 (SEQ ID NO: 47), pLybAL19 (SEQ ID NO:48), pLybAL21 (SEQ ID NO: 49), and pLybAL22 (SEQ ID NO: 50). In someembodiments, the transformed host cyanobacterium comprises pLybAL28 (SEQID NO: 121), pLybAL29 (SEQ ID NO: 122), pLybAL30 (SEQ ID NO: 123), andpLybAL23 (SEQ ID NO: 118).

Sugar Secretion

In various embodiments, a transformed disaccharide-accumulatingphotosynthetic microorganism can secrete the accumulated disaccharidefrom within the cell into its growth environment. Secretion of thedisaccharide can be an inherent effect of transforming thephotosynthetic microorganism to accumulate a disaccharide or thephotosynthetic microorganism can be further engineered to secrete thedisaccharide. For example, some cyanobacteria transformed to accumulatetrehalose inherently secrete trehalose from the cell (see e.g., Examples19-20). As another example, a cyanobacterium transformed to accumulatesucrose can be further engineered to secrete sucrose from the cell (seee.g., Example 16).

A host photosynthetic microorganism, such as a cyanobacterium, can befurther engineered to secrete a disaccharide. In some embodiment, atransformed host photosynthetic microorganism is engineered to express aporin specific for the accumulated disaccharide. For example, acyanobacterium engineered to accumulate sucrose can be furtherengineered to express a sucrose porin (see e.g., Example 16). In oneembodiment, the transformed disaccharide-accumulating cyanobacteriumcomprises an scrY nucleic acid, such as SEQ ID NO: 94. In oneembodiment, the transformed disaccharide-accumulating cyanobacteriumcomprises a nucleic acid encoding a scrY polypeptide, such as SEQ ID NO:95. In one embodiment, the transformed disaccharide-accumulatingcyanobacterium comprises a plasmid containing scrY, such as pLybAL32(SEQ ID NO: 91). It is contemplated that a similar approach can beapplied to other photosynthetic microorganisms or other targetdisaccharides.

Modulation of Sugar Degradation

In some embodiments, a host photosynthetic microorganism, such as acyanobacterium, is further engineered to improve disaccharide productionby modulation of degradation activity (see e.g., Example 14). In someembodiments, an invertase homologue can be down-regulated or eliminatedin a transformed photosynthetic microorgansim. For example an invertasehomologue from Synechocystis spp. PCC 6803 (nucleotide sequence SEQ IDNO: 70; polypeptide sequence SEQ ID NO: 71) can be down-regulated oreliminated in a transformed cyanobacterium. As another example, aninvertase homologue from Synechococcus elongatus PCC 7942 (nucleotidesequence SEQ ID NO: 72; polypeptide sequence SEQ ID NO: 73) can bedown-regulated or eliminated in a transformed cyanobacterium. In someembodiments, a sucraseferredoxin-like protein is down-regulated oreliminated in a transformed cyanobacteriuma. For example, asucraseferredoxin-like protein from Synechocystis spp. PCC 6803(nucleotide sequence SEQ ID NO: 74; polypeptide sequence SEQ ID NO: 75)(Machray G. C. et al. 1994. FEBS Lett 354, 123-127) can bedown-regulated or eliminated in a transformed cyanobacterium. Thesegenes can be deleted using the markerless deletion protocol describedin, for example, FIG. 11 (see e.g., Examples 12-13) A similar approachcan be taken for other disaccharides engineered to be accumulated in acyanobacterium.

Other methods of down-regulation or silencing the above genes are knownin the art. For example, disaccharide degradative activity can bedown-regulated or eliminated using antisense oligonucleotides, proteinaptamers, nucelotide aptamers, and RNA interference (RNAi) (e.g., smallinterfering RNAs (siRNA), short hairpin RNA (shRNA), and micro RNAs(miRNA) (see e.g., Fanning and Symonds (2006) Handb Exp Pharmacol. 173,289-303G, describing hammerhead ribozymes and small hairpin RNA; Helene,C., et al. (1992) Ann. N.Y. Acad. Sci. 660, 27-36; Maher (1992)Bioassays 14(12): 807-15, describing targeting deoxyribonucleotidesequences; Lee et al. (2006) Curr Opin Chem Biol. 10, 1-8, describingaptamers; Reynolds et al. (2004) Nature Biotechnology 22(3), 326-330,describing RNAi; Pushparaj and Melendez (2006) Clinical and ExperimentalPharmacology and Physiology 33(5-6), 504-510, describing RNAi; Dillon etal. (2005) Annual Review of Physiology 67, 147-173, describing RNAi;Dykxhoorn and Lieberman (2005) Annual Review of Medicine 56, 401-423,describing RNAi). RNAi molecules are commercially available from avariety of sources (e.g., Ambion, Tex.; Sigma Aldrich, Mo.; Invitrogen).Several siRNA molecule design programs using a variety of algorithms areknown to the art (see e.g., Cenix algorithm, Ambion; BLOCK-iT™ RNAiDesigner, Invitrogen; siRNA Whitehead Institute Design Tools,Bioinofrmatics & Research Computing). Traits influential in definingoptimal siRNA sequences include G/C content at the termini of thesiRNAs, Tm of specific internal domains of the siRNA, siRNA length,position of the target sequence within the CDS (coding region), andnucleotide content of the 3′ overhangs.

In some embodiments, a host photosynthetic microorganism can be furtherengineered to promote disaccharide secretion from the cells. Forexample, a cyanobacterium can be further engineered to promote sucrosesecretion from the cells (see e.g., Example 15-16). When in a lowosmotic environment, the sucrose can be automatically expunged from thecells, as done with osmoprotectants by some organisms when transitioningfrom high to low salt environments (Schleyer, M., Schmidt, R. andBakker, E. P. 1993. Arch Microbiol 160, 424-43; Koo, S. P., Higgins, C.F. and Booth, I. R. 1991. J Gen Microbiol 137, 2617-2625; Lamark, T.,Styrvold, O. B. and Strgim, A. R. 1992. FEMS Microbiol. Lett 96,149-154). Sucrose porins can be engineered to be expressed in atransformed cyanobacterium (see e.g., Example 16). These genes can becloned and transformed into cyanobacteria according to techniquesdescribed above. Such approaches can be adapted to other photosyntheticmicroorganisms.

In some embodiments, a host photosynthetic microorganism is transformedby stable integration into a chromosome of the host. For example, a hostcyanobacterium can be transformed by stable integration into achromosome of the host (see e.g., Examples 11-13). Chromosomalintegration can insure that the target gene(s) is installed into theorganism without risk of expulsion as sometimes occurs withplasmid-based gene expression. Chromosomal integration can also reduceor eliminate the need for antibiotics to maintain target genes.

Preferably, the strategy for chromosomal integration targets geneinsertion into what is termed the upp locus on the chromosome (see e.g.,Example 11-13). This site codes for the enzyme uracilphosphoribosyltransferase (UPRTase) which is a scavenger enzyme inpyrimidine biosynthesis. Using this strategy allows candidate selectionby 5-fluorouracil (5-FU), which can eliminate non-integrated organisms.Segregation methods are generally used in cyanobacterial systems becausethese organisms contain multiple copies of their chromosomes (e.g., upto 12 for Synechocystis spp. PCC 6803 and 16 for Synechococcus elongatusPCC 7942). This strategy is particularly attractive for cyanobacteria,because this approach can avoid the use of traditional segregationtechniques that rely on selective pressure and statistical integrationfor successful segregation. Using 5-FU as a screening agent can be moreefficient because it can prevent growth for any organism that containseven a single active upp gene. In this manner, fully integratedcandidates can be selected rapidly over fewer generation cycles comparedto the processes required of traditional techniques.

Solid Phase Photosynthetic Bioreactor

Provided herein is a photobioreactor for culturing photosyntheticmicroorganisms comprising a solid phase cultivation support for thegrowth of photosynthetic microorganisms. A solid phase cultivationsupport, or solid cultivation support, or solid support, or the like, isgenerally understood to mean a cultivation support that is neither aliquid nor a gas. Although the support itself is a solid, the supportstructure may be selected so that it absorbs a liquid (e.g., growthmedia), a gas, or both. In certain preferred embodiments, as describedmore fully below, the solid support can absorb moisture for use by themicroorganisms during cultivation.

Various embodiments of the photobioreactor(s) described herein cansupport the growth a photosynthetic microorganism. The photosyntheticmicroorganism grown in the photobioreactor can be, for example, anaturally photosynthetic microorganism, such as a cyanobacterium, or anengineered photosynthetic microorganism, such as an artificiallyphotosynthetic bacterium. Exemplary microorganisms that are eithernaturally photosynthetic or can be engineered to be photosyntheticinclude, but are not limited to, bacteria; fungi; archaea; protists;microscopic plants, such as a green algae; and animals such as plankton,planarian, and amoeba. Examples of naturally occurring photosyntheticmicroorganisms include, but are not limited to, Spirulina maximum,Spirulina platensis, Dunaliella salina, Botrycoccus braunii, Chlorellavulgaris, Chlorella pyrenoidosa, Serenastrum capricomutum, Scenedesmusauadricauda, Porphyridium cruentum, Scenedesmus acutus, Dunaliella sp.,Scenedesmus obliquus, Anabaenopsis, Aulosira, Cylindrospermum,Synechoccus sp., Synechocystis sp., and/or Tolypothrix.

Preferably, the bioreactor is configured to support innoculation,growth, and/or harvesting of cyanobacteria transformed to accumulate adisaccharide, as described above.

The photobioreactor can be an open or a closed system, as described morefully below. In various embodiments, the photobioreactor includes asolid phase cultivation support, a protective barrier layer, and asuspension element. Some embodiments of the photobioreactor can containa system for delivery and/or removal of gas, fluids, nutrients, and/orphotosynthetic microorganisms. Delivery systems can be, for example,standard plumbing fixtures. Any of the various lines can includequick-connect plumbing fixtures. The photobioreactor can have a gasdelivery line, which can deliver, for example, delivering carbon dioxideor normal atmospheric air. The photobioreactor can have a fluid deliveryline. Preferably, the fluid delivery line connects to a trickle or dripsystem which conveys a fluid (e.g., water) to the solid phasecultivation support. The photobioreactor can have a nutrient deliveryline. Formulation of a nutrient composition for the growth andmaintenance of a photosynthetic microorganism is within the ordinaryskill of the art. In some embodiments, the nutrient and fluid deliverylines can be combined, for example to supply a fluid-based nutrientmixture. In some embodiments, the fluid delivery line or the nutrientdelivery line can be a spray device for distributing a liquid mediumover the growth surface. In such spray devices, the photobioreactor islarge enough to accommodate, for example, a spray device between anouter layer, such as a barrier layer, and the solid phase cultivationsupport. Usually, nutrients are supplied in a water-based composition.It can be advantageous to provide for different water delivery line(s)and nutrient delivery line(s) so as to provide for independent controlof moisture and nutrient levels. The photobioreactor can have a productharvest line so as to provide for collection of photosyntheticmicroorganisms and/or liquid suspended/soluble products. Thephotobioreactor can have an inoculation line so as to provide forinoculation of photosynthetic microorganisms. In some embodiments, thefluid, nutrient, and/or inoculation lines can be combined.

One embodiment of a solid-phase photobioreactor is depicted in FIG. 1(front view) and FIG. 2 (side view). In these embodiments, a solid phasecultivation support 2 is enclosed by protective barrier 7. FIG. 2 showsthat the solid cultivation support is between protective barrier layers3 that comprise the protective barrier 7. The solid cultivation support2 provides the surface upon which photosynthetic microorganisms arecultivated. The protective barrier layers 3 that make up the protectivebarrier 7 are transparent to allow actinic radiation to reach thesurface of the solid cultivation support 2 to support the growth ofphotosynthetic microorganisms. Resealable closures 4 allow for aprotective barrier 7 that is releasably sealed. Exchange of gases andvapor occurs through a selective panel 5 of material that isincorporated into the protective barrier 7. The photobioreactor 1 can besuspended by support elements 6 to allow for a vertical ornon-horizontal orientation.

Another embodiment of a solid-phase photobioreactor is depicted in FIG.12A (front view) and FIG. 12B (side view). The reactor 1 can be designedin a segmented format, which can aid in servicing and minimizespotential contamination of the surface and/or plumbing. Each segment canbe connected to the reactor through plumbing (e.g., quick connect typeplumbing) of the various supply and product harvest lines. The reactorcan be supported by a suspension element 6 from, for example, rails,which allows the reactor 1 to hang in space and aid in rapid servicingof each segment. The outer protective barrier 7 can be a transparentmaterial that enables light penetration facilitating photosynthesis onthe growth surface 2, while preventing environmental contamination andmoisture loss from evaporation. The growth surface 2 can be composed ofa material that retains moisture, supplies nutrients, removes products,and/or enables high density growth of photosynthetic microorganisms. Thegrowth surface 2 can be serviced by plumbing that provides continuousfeeding/product harvest from the surface by liquid culture media. Themedia tubing 8 can be a porous hose that seeps liquid to the surface 2,which can percolate through the growth surface 2 by gravity. The liquidcan be harvested at the bottom of the reactor by a harvesting tube 9,which collects products and excess liquid media for transport from thereactor 1. Gases, such as carbon dioxide and air, can be supplied to thereactor by a gas dispersion tube 10. The gas supply tube 10 can providea positive pressure environment and is expected to supply gasesnecessary for growth in a controlled, efficient manner. The gas supplyline 10 can also assist in minimizing moisture loss by humidifyingincoming gas streams. Excess gas from the reactor can be vented by abreathable panel 5 (on the reverse side, not shown) that is a porousmaterial that allows for gas passage but minimizes or eliminatesenvironmental contamination. Contamination is expected to be minimizedby the positive pressure configuration of the reactor 1 throughfiltration of the incoming gas delivered by the supply line 10. Positivepressure can also prevent contamination from the environment byproviding an inside out pathway for gas flow.

In the embodiment depicted in FIG. 12B, features of the reactor 1 aredepicted in an orientation relative to the growth surface. Thebreathable panel 5 allowing for excess gas to escape the reactor 1 canbe located toward the bottom of the device to provide a path for gas tomigrate across the growth surface 2. Location of the breathable panel 5on the bottom of the barrier surface 7 also minimizes or prevents thepossibility of carbon dioxide segregation and build up resulting fromits higher density relative to air. The dimensions of the breathablepanel 5 can be determined based on gas flow rate requirements foroptimal growth on the cultivation surface 2.

Solid Phase Cultivation Support

The solid phase cultivation support of a photobioreactor as describedherein provides a surface on and/or in which a photosyntheticmicroorganism can grow. Preferably, the solid phase cultivation supportcomprises a material that provides or facilitates the provision and/orretention of moisture and/or nutrients to the organisms, so as topromote and sustain growth. Embodiments of the invention are not limitedto the type or strain of photosynthetic microorganisms that can becultivated. One of ordinary skill in the art will recognize that theamount of moisture and the amount and composition of nutrients desirablefor cell growth will vary with the type or strain of photosyntheticmicroorganism and the application for which it is to be grown. Materials(or the substances contained within or on those materials) that may havea deleterious effect on the growth of photosynthetic microorganisms aregenerally avoided.

A single photobioreactor can be used to cultivate a single type ormultiple types or strains of photosynthetic microorganisms. Further, thesolid cultivation support can comprise material(s) such that it issuitable for a single cultivation cycle or multiple cycles ofcultivation, with or without sterilization between cultivation cycles.Still further, a photobioreactor can be configured to cultivate a singletype or strain of microorganism or multiple types or strains ofmicroorganisms on a single or multiple solid supports. In someembodiments, instead of an axenic culture, a community of differentphotosynthetic microorganisms, or a community of photosynthetic andnon-photosynthetic microorganisms, can be grown together simultaneouslyon one cultivation support. A single photobioreactor can also comprisemultiple cultivation supports. Thus in another embodiment, multiplecultivation supports within a single protective barrier can cultivateone or more types or strains of photosynthetic microorganismssimultaneously.

The solid cultivation support preferably comprises a relatively porousmaterial. A relatively porous material generally has increased surfacearea and can retain and/or absorb more moisture than a relativelynon-porous material. Also preferred is a solid cultivation support thathas a textured or topographical surface(s). A textured or topographicalsurface can enhance cell density compared to a relatively non-texturedor smooth surface. Although the choice of support material and surfacetopography are typically selected to enhance the adhesion ofmicroorganisms to the support, it generally is desirable that theorganisms not so tightly adhere so as to impede their removal orharvest. In some embodiments, the solid cultivation support comprises amaterial suitable for adhesion and growth of microorganisms. In someembodiments, the solid cultivation support comprises a material thatreduces or eliminates biofilm formation.

The solid-phase supports of the photobioreactors described herein arebelieved to be different from solid supports that have been utilized inthe art (e.g., the most commonly used solid phase support for the growthof microorganisms is agar). Agar is generally cast into rigid forms,such as a petri dish, and used while therein to maintain its physicalintegrity because agar tends to break or tear when subjected to minimallevels of stress, strain, or both. In contrast, various embodiments ofthe cultivation support is sufficiently strong and durable that it canbe used in a photobioreactor while maintaining its physical integritywithout the need of a stronger, more durable “frame”. Or stated anotherway, the prior art involved a sufficient portion of the weak agarsupport in contact with a substantially stronger, more durable material(e.g., a petri dish) such that a composite is formed. Thus, thesolid-phase supports of various embodiments of the photobioreactor aresuitable in themselves for the cultivation of microorganisms and aresufficiently strong and durable.

Other desirable physical characteristics and/or operation parameters ofthe solid-phase support are described below. For example, the supportcan be relatively flat and rigid (like a plate) or it may consist of amultiplicity of flat and rigid sections flexibly connected by, e.g.,hinges, springs, wires, threads, etc. Suitable rigid materials include,but are not limited to, various metals, polymers, ceramics, andcomposites thereof. The rigid materials preferably have surfacetopographies that enhance the adherence of the photosyntheticmicroorganisms thereto. Further, the rigid materials may be formed witha desired level of porosity to enhance the ability to deliver moistureand/or nutrients to the photosynthetic microorganisms. Still further,the rigid materials may be coated with absorbent or super absorbentpolymer formulations (see below). Alternatively, the support may consistessentially of flexible material, such as a fabric. Fabrics for use in asolid-phase support include, but are not limited to, cotton, polyester,and/or cotton polyester blends, optionally coated with absorbent orsuper absorbent polymer formulations. Flexibility of the cultivationsupport can be greatly advantageous because it allows for thecultivation support to be folded, twisted, draped, or rolled forstorage, transport, or handling.

In addition, the solid-phase cultivation support is preferablystructurally stable at elevated temperatures (e.g., about 120° C. andabove), such as would be typically encountered during autoclavesterilization, and will not melt like agar. Thus, in one embodiment, thecultivation support may be sterilized by autoclaving and then placedwithin the protective barrier of the invention. In another embodiment,the cultivation support can be placed within the protective barrier, andthe entire photobioreactor may then be autoclaved. Although autoclavingis one method for sterilization, one of skill in the art will recognizethat any other appropriate method of sterilization may be utilized.

The solid cultivation support of the present invention can comprise orbe made of any material appropriate for supporting the growth ofphotosynthetic microorganisms. For example, the support may be composedof natural materials, modified natural materials, synthetic materials,or any combination thereof. Natural materials can include, but are notlimited to cotton, wool, processed woven plant fibers, and naturalpolysaccharides (e.g., agar, starches, cellulosics). Modified naturalmaterials can include, but are not limited to, chemically modified plantfibers such as nitrocellulose or cellulose esters, in addition tonatural fibers co-woven or blended with polyester or polyamide fibers.Synthetic materials can include, but are not limited to, fibers composedof nylon, fiberglass, polysiloxanes, polyester, polyolefins, polyamide,copolyester polyethylene, polyacrylates, or polysulfonates. Furtherexamples of solid cultivation support materials include wire mesh,polyurethane foams, polyethylene foams, vitreous carbon foams,polyester/polyethylene foams, polyimide foams, polyisocyanate foams,polystyrene foams, and polyether foams, or combinations thereof.

In various embodiments, the solid cultivation support is a fabric. Thefabric can be formed by methods such as, but not limited to, weaving,knitting, felting, and the bonding or cross-linking of fibers orpolymers together. The construction of the fabric can be loose or open.Alternatively, the fabric can be tightly constructed. That said, fabricsthat have a significant texture, surface area, topographicalvariability, and/or roughness may provide more mechanical bonding oradherence of the photosynthetic microorganisms to the cultivationsupport and thus may be preferable, especially in embodiments whereinthe photobioreactor is handled, transported, or otherwise moved duringthe process for inoculating the support with, and/or growing and/orharvesting the organisms. Preferably, in most applications the adherenceof the organisms to the substrate should not be so great as to undulyhinder their removal during a harvesting operation. Still further, theability of a fabric to retain moisture and/or nutrients for use by theorganisms can be controlled by selecting fibers that are generallyhydrophobic, hydrophilic, or a mixture of such fibers. These propertiesallow for moisture and/or nutrients dissolved therein to be retainedand/or transported by the solid support so that they are available tothe microorganisms growing on the surface.

The properties of the cultivation support, especially moisture and/ornutrient retention, can be enhanced by coating the support with amaterial selected to enhance photosynthetic microorganism growth. Forexample, the cultivation support can be coated with agar or a superabsorbent polymer such as modified cellulose ester, acrylate oracrylate/polyamine copolymer blends. These coating materials aretypically able to absorb and retain greater than 10 to 100 times theirdry weight in water. In some embodiments, these materials are formulatedsuch that they would retain their superabsorbent properties in thepresence of ionic culture media components. The coating material cancoat the surface of the cultivation support, or the fibers of a fabricif used, or both. In one embodiment, a swatch of terrycloth serving asthe cultivation support is coated in agar. When a solid cultivationsupport is coated as such, the “surface” of the cultivation supportincludes the surface of the coating if photosynthetic microorganismsattach to such. To keep the cultivation support thin, pliable, andlight, the coating is preferably thin, for example, no greater thanabout 100 microns. However, thicker coatings can also be used dependingon the application desired, or on the combination of solid cultivationsupport and coating material selected.

The solid-phase cultivation support can be a composite, layeredstructure. The solid-phase cultivation support can comprise at least twolayers arranged so as to be adjacent. Multiple layers of the solid-phasecultivation support can be coupled, such as by bonding, stitching,adhesive, compression, or any other suitable means. The various layerscan each independently be selected from among the several materialsdiscussed above. For example, the solid-phase cultivation support cancomprise a first material layer of fabric bonded to a second materiallayer of synthetic foam. An another example, the solid-phase cultivationsupport can comprise a first material layer of synthetic foam bonded toa second material layer of synthetic foam of the same or differentdensity. Preferably, the solid-phase cultivation support is a composite,layered structure comprising at least a first layer, which is composedof a high surface area growth material, and a second layer, which iscomposed of a permeable type material.

In addition to supplying moisture, nutrients, and a surface forattachment, the cultivation support can provide a surface for capturingactinic radiation. Thus, in some embodiments, the dimensions of thesolid cultivation support are sheet-like. That is, the depth of thesupport is small relative to the length and width of the support. In oneembodiment, the cultivation support is a sheet-like layer betweenfilm-like layers of a protective barrier. Such a flat bioreactor can besuspended like a flat panel. In another embodiment, just the cultivationsupport is suspended like a curtain enclosed by the outer barrier of thephotobioreactor. A thin sheet of a traditional solid phase support suchas agar would easily rip apart, and would likely not be able to besuspended as such. Therefore, it is preferable that the solidcultivation support alone be able to maintain its integrity whensuspended, even when saturated with liquid.

As shown herein, a fabric with a terrycloth-type weave can provide asuitable solid support (see e.g., Example 1). One of skill in the artwill understand that other natural, modified-natural, and syntheticmaterials may also be acceptable. Terrycloth provides many of theattributes believed to be desirable in a solid support of the presentinvention. For example, it is flexible, and not prone to tearing,ripping, breaking, or cracking when handled in accordance withnon-destructive techniques (e.g., bending, folding, twisting, orrolling) under conventional conditions (e.g., temperature). Likewise,terrycloth is typically not prone to tearing, ripping, or breaking whenmodestly stretched (even when saturated with liquid). Additionally,terrycloth tends to be highly textured because it is composed of themany loops of fibers. This provides a large amount of surface area forthe attachment of microorganisms thereby increasing the amount ofmicroorganisms that can be grown on a support of any given size.Further, a cotton terrycloth typically absorbs at least about threetimes its own weight, which allows for moisture and any nutrientsdissolved therein to be retained by the fabric support so that they areavailable to the microorganisms growing on the surface of the support.Thus, various embodiments provide for a solid cultivation support thatis thin or sheet-like in dimension, able to support its own wet weightwhile suspended, flexible, pliable, absorbent, highly textured, or anycombination thereof.

The above-described supports can be, and in many applications preferablyare, used repeatedly and more preferably for so long as they arestructurally sound and provide a surface adequate to support the growthof the microorganisms disposed of after a single use thereby reducingoperational costs and waste. That said, there can be certainapplications in which single-use supports would be desirable, such ascultivation of recombinant photosynthetic microorganisms useful inproducing pharmaceutical products such as small organic molecules ortherapeutic proteins and peptides. To reduce the costs of suchsingle-use supports and in view of the fact that that they will not bereused, such supports need not be as durable and therefore can be madeor constructed using methods and/or materials that are less costly andless durable. For example, supports comprised of paper fibers similar tothat of paper towels may be appropriate.

Several embodiments of a solid phase cultivation support are depicted inFIG. 13. The solid phase cultivation support material depicted in FIG.13A is a single material that can provide sustainable surface fororganism growth, access to moisture and nutrients, point of organismattachment, and/or removal of cultivation products. The material canallow for liquid percolation and equilibrium diffusion to exchangenutrients, moisture, and products between the surface and organisms. Therendering of the structure configuration is an example of a high surfacearea material, which can be optimized for dimension and shape. The solidphase cultivation support material depicted in FIG. 13B is a hybridmaterial that is composed of multiple layers of materials, each havingspecific functions for the growth surface. The base layer can be aporous material that efficiently allows for supply of nutrients andmoisture as well as removal of products that are percolated through thematerial. The base material can also provide physical support for thegrowth surface. The outer layer(s) is expected to be attached to thebase layer and can be optimized to provide point of attachment for theorganisms. The surface layer can achieve more control of the surfacegrowth environment in terms of surface area and compatibility with thecultivated organism.

Protective Barrier

A photobioreactor as described herein can comprise a barrier thatprotects the solid cultivation support and growth surface fromcontamination and/or moisture loss. At the same time, thephotobioreactor provides for actinic radiation, either sunlight orartificial light, and carbon dioxide reaching the photosyntheticmicroorganisms. In various embodiments, the photobioreactor comprises atleast one solid support and a protective barrier for the cultivation ofphotosynthetic microorganisms.

Protection from Physical Handling and/or Contamination

To prevent contamination, a protective physical barrier can at leastpartially cover the solid cultivation support. In certain embodiments,the physical barrier can enclose the cultivation support. The protectivebarrier can also control, at least in part, the loss of the moisturefrom the support and/or the atmosphere within the photobioreactor to theatmosphere outside the photobioreactor. One of skill in the art willrecognize that the protective barrier can be constructed from any ofnumerous types of materials depending on the embodiment of the inventiondesired.

The protective barrier can completely enclose the cultivation support.If the protective barrier is permanently sealed, the barrier must bebreached, cut, torn, or the like to access the cultivation supportwithin. Thus, in some embodiments, access is provided through theprotective barrier to the cultivation support and the surface on whichthe microorganisms are grown.

In preferred embodiments, the protective barrier is releasably sealed.The releasable seal can be any of a number of closure types including,but not limited to zipper-type closures such as found in Ziploc® storagebags (SC Johnson Company), hook-and-loop type fasteners (e.g., VelcroUSA, Inc.), twist ties, zipties, snaps, clips, pressure sensitiveadhesive backed surfaces, and all art recognized equivalents thereto. Acomplete seal, however, is not necessarily required; and it may be moreefficient not to completely seal the outer barrier to allow for easieraccess to the cultivation support.

The photobioreactor can comprise a single cultivation support ormultiple cultivation supports within a protective barrier. In someembodiments, a single cultivation support is enclosed within a singleprotective barrier. For example, a plastic bag may form a protectivebarrier within which a single solid cultivation support is enclosed (seee.g., FIG. 1). In other embodiments, a single protective barrier mayenclose multiple solid cultivation supports. For example, agreenhouse-type structure may form a protective barrier within whichmultiple solid cultivation supports are enclosed.

Transmission of a Actinic Radiation

The photobioreactor can provide for transmission of actinic radiation,either sunlight or artificial light, to the photosyntheticmicroorganisms. But the protective barrier of the invention need notnecessarily be transparent to light. Some embodiments can comprise acultivation support enclosed within a non-transparent protective barrierif a sufficient light source for the growth of photosyntheticmicroorganisms is provided within. It may be desirable, simpler, moreeconomical, and the like to provide a transparent barrier to utilizesunlight, for instance, as a light source.

Preferred embodiments provide for a transparent barrier comprising amaterial such as, but not limited, glass or any type of transparent orgenerally visible light transmitting polymer such as polyethylene,acrylic polymers, polyethylene terephthalate, polystyrene,polytetrafluoroethylene, or co-polymers thereof, or combinationsthereof. The transparent barrier can be selected from materials that aredurable and not prone to ripping, tearing, cracking, fraying, shredding,or other such physical damage. The transparent barrier material can beselected for its ability to withstand autoclave sterilization or otherexposure to temperature extremes. Further, the transparent barriermaterials can be selected to withstand prolonged exposure to sunlight orother radiation without discoloring or deteriorating. One of skill inthe art will recognize that certain coatings or formulations that resistphotooxidation can be particularly useful. In addition, infraredreflecting or absorbing coatings can be selected to reduce and/orotherwise regulate the buildup of temperature within the photobioreactorof the invention.

One of skill in the art will recognize that the thickness of thetransparent barrier material will vary depending on mechanicalproperties of scale. For example, the transparent barrier material maybe of an industrial/marine type plastic about 10 mil thick or it may beof the type used in a household plastic bag, i.e., around 2 mil thick.In one embodiment, the transparent barrier material is thin andflexible. For example, the transparent barrier material can be less thanabout 10 mil.

In some embodiments, the barrier forms a protective layer or filmcovering the two sides of a thin, flexible, solid cultivation support.The assembled photobioreactor of this embodiment would be flexible, andcould be bent, rolled, folded, twisted, or the like for storage,transport, conveying, or handling. In another embodiment, thetransparent barrier material is rigid. For example, the barrier can be aglass greenhouse. Most likely, the thickness of the greenhouse glasswould preferably be consistent with building practices but it ispossible that it could be altered. The photobioreactor of such anembodiment would be for practical purposes immovable, but multiple solidsupports could be handled, transported, conveyed and the like within theconfines of one protective, transparent barrier.

Although a protective barrier can be selected to provide sufficientlight for the growth of photosynthetic microorganisms, it is notnecessary that the entire barrier be transparent. Thus, in someembodiments, portions of the barrier, such as one or more edges, aremade from a non-transparent material. The non-transparent material canbe composed of materials including, but not limited to polyethylenefiber material (Tyvek®), polytetrafluoroethylene filtration media,cellulosic filter material, fiberglass filter material, polyester filtermaterial and polyacrylate filter material, and combinations thereof. Thenon-transparent material can be selected for durability. In such anembodiment, a transparent portion of the barrier would be furtherprotected from tearing, ripping, fraying, shredding, and the like by adurable, non-transparent portion. In one embodiment, a non-transparentportion provides or comprises an attachment structure and/orreinforcement for suspending the photobioreactor by further comprisingmounting or attachment points (e.g., holes, loops, hooks, grommets, orother art equivalent device, opening or, recess) and/or or a mechanismfor securing the photobioreactor to a structure. Although it is notrequired that any such mounting points, etc., be located in or on thenon-transparent portion, they can be contained within or on anon-transparent portion of the barrier, within or on a transparentportion of the barrier, or within or on a non-transparent and atransparent portion of the barrier. The attaching structure may also becontained within or on, or pass through, the solid cultivation support.

In some embodiments, the device has a discernable front side and backside. The front side of this device is meant to face a light source, andthus the portion of the barrier on the front side is preferablytransparent, while the portion of the protective barrier on the sidefacing away from the light source is not necessarily transparent.

Provision of Gas Exchange

During photosynthesis, photosynthetic microorganisms consume carbondioxide and release oxygen. A photobioreactor as described herein canprovide carbon dioxide sufficient for a desired amount of photosynthesisto occur. One way to supply carbon dioxide to the inside of thephotobioreactor is to allow direct gas exchange between the air insideand the air surrounding the photobioreactor. For example, holes, vents,windows, or other such openings can be provided in the protectivebarrier so that the system is open to the surrounding atmosphere.

But such an open configuration may not be desirable when contaminationof the photosynthetic microorganisms is a concern. To address thisconcern, the protective barrier can completely seal off the solidsupport or supports enclosed within from the outside air. In such anembodiment, the desired concentration of carbon dioxide can bemaintained by introducing it into the enclosure. For example, one ofskill in the art would recognize that plumbing or tubing from a tank ofcompressed carbon dioxide would allow for carbon dioxide to be mixedinto the air enclosed within the photobioreactor. In addition, it isknown that the emissions from factories, industrial plants, powerplants, or the like can be harnessed as a source of carbon dioxide forphotosynthetic microorganisms, thus reducing carbon emissions. In oneembodiment, a gas supply line can provide carbon dioxide to the growthsurface local area.

It may be desirable, simpler, more economical, and the like to provide aselective barrier that is gas permeable to utilize atmospheric carbondioxide. Thus, some photobioreactor embodiments provide for a selectivebarrier that allows gas and vapor exchange between the environmentenclosed within the protective barrier and the surrounding air, whilestill providing a sealed physical barrier against contamination.

Such barrier can be at least partially gas/vapor permeable (e.g., muchless permeable than conventional textile fabrics, higher than that ofplastic films, and/or similar to that of coated papers), thus allowingthe exchange of gases such as carbon dioxide and oxygen but isadditionally at least partially and preferably considered to beimpermeable to solids and liquids. In some embodiments, thephotobioreactor can contain a semi-permeable barrier layer and a gassupply line to maintain an elevated carbon dioxide concentration in thearea around or near the growth surface.

In some embodiments, a selective barrier can have an average pore sizeor diameter of no greater than about 10 micrometers and a gas exchangerate that is at least about 5 and no greater than about 10,000 Gurleyseconds (a Gurley second or Gurley is a unit describing the number ofseconds required for 100 cubic centimeters of gas to pass through 1.0square inch of a given material at a given pressure differential).Therefore, in addition to allowing gas exchange, the selective barriercan prevent loss of moisture from the enclosed system.

The selective barrier portion of the protective barrier can be composedof any appropriate polymer-based material, such as spunbonded olefinbarriers. Spunbonded olefin barriers (very fine polyethylene fibers)with various properties are readily available from DuPont under thebrand name Tyvek®. Such materials are particularly advantageous becauseof their combination of physical properties, i.e., they tend to resistthe transmission of liquids such as water yet they have a sufficientlyhigh degree of gas/vapor permeability; they are relatively strong,absorb little or no moisture, are rip-resistant, have a significantdegree of elasticity, and are highly flexible. Spunbonded olefin canexceed 20,000 cycles when tested on an MIT flex tester (TAPPI methodT-423). In addition, they are inert to most acids, bases and saltsalthough a prolonged exposure to oxidizing substances, such asconcentrated nitric acid or sodium persulfate, will cause some loss ofstrength. Spunbonded olefin barriers have good dimensional stability inthat sheet dimensions tend to change less than 0.01% between 0 and 100%relative humidity at constant temperature. Certain products meet therequirements of Title 21 of the United States Code of FederalRegulations (21 CFR 177.1520) for direct food contact applications. Theyalso have excellent mold and mildew resistance; and are of a neutral pH.Unfortunately, however, their UV resistance is not exceptional. Thatsaid, at least one to three months of useful outdoor life can usually beexpected. Additionally, their UV resistance can be improved with opaquecoatings or by including UV inhibitors in the polymer fibers.Additionally, because the spunbonded olefins produced to date areopaque, the portion of the protective barrier that would comprise suchmaterial is preferably not situated and/or so extensive as to compromisethe cultivation of the photosynthetic microorganisms.

In particular, spunbonded olefin can be produced in “hard” and “soft”structure types. Type 10, a “hard,” area-bonded product, is a smooth,stiff non-directional paper-like form. Types 14 and 16 are “soft,”point-bonded products with an embossed pattern, providing a fabric-likeflexible substrate. Type 14 styles (or the equivalent thereof) can beused, for example, where barrier, durability, and breathability arerequired. Type 16 styles are pin perforated with 5-20 mil (0.13-0.51 mm)holes, giving them much higher air and moisture permeability, additionalsoftness, and greater flexibility and drape than Type 14 styles, but atthe expense of lower tear strength and barrier properties. Thus, theparticular properties of the selective barrier can be customized byselecting one or more types of spunbonded olefin products.

Other examples of selective polymer barriers include, but are notlimited to nylon, polysulfone, polytetrafluoroethylene, cellulosic,fiberglass, polyester and polyacrylate membranes and filter material,and combinations thereof.

The entirety of the protective barrier need not be gas permeable toprovide for a barrier that is sufficiently selective for the growth ofphotosynthetic microorganisms. Only a portion of the protective barriersufficient to allow for adequate gas exchange need be gas permeable. Inone embodiment, the selective portion is a panel of the protectivebarrier (see e.g., FIG. 1). The size and placement of the selectivepanel in relation to the area of the support surface can be altered toachieve a desired amount of gas exchange for a particular applicationwithout unduly hindering the cultivation of the microorganisms. One ofskill in the art will recognize that the percentage of the area of theouter barrier composed of the gas permeable selective material willdepend on the gas permeability rate of the material. In fact, becausethe gas permeable portion will still allow the transport of water vaporacross it, in various embodiments, the size of the gas permeable portionof the protective barrier is selected so as to allow for sufficienttransport of oxygen and carbon dioxide while minimizing the loss ofmoisture.

Suspension and Conveyance System

Photobioreactors described herein can be configured for large scaleproduction and/or harvesting through, for example, integration into ahandling and conveyance system. FIG. 3 shows an above view of anexemplary design of a photobioreactor farm for handling large numbers ofphotobioreactors in a continuous process. The photobioreactors orcultivation panels (not individually shown) are attached to conveyorsystems 8. The conveyor systems 8 move the cultivation panels alongtheir paths. Multiple conveyor systems converge at centrally locatedinoculation and harvesting centers 9. Thus, the cultivation panels aremoved into the inoculation and harvesting centers 9 where they can beprocessed (e.g., harvested and/or inoculated) and then the panels aremoved away from the centers following inoculation and during the periodof cultivation of the biomass. The panels are then moved back towardsthe centers during the latter period of cultivation prior to harvesting,eventually arriving back at the centers with mature biomass for harvest.The cycle is then repeated. Harvested biomass can be transported througha pipeline 10 for further processing. The capacity of thephotobioreactor farm can be increased by adding additional conveyorsystems or additional inoculation and harvest centers to form largearrays dedicated to biomass production.

Suspension of Photobioreactor

To supply light to photosynthetic microorganisms, a favored embodimentof the photobioreactor is one in which the cultivation support is thinand sheet-like. When oriented horizontally, the efficient utilization offloor space tends to decrease, therefore in certain embodiments of theinvention the cultivation support is oriented non-horizontally,preferably substantially vertically, or more preferably vertically.Nevertheless, the cultivation support may be oriented in essentially anymanner so long as a sufficient amount of actinic radiation can reach themicroorganisms. Thus, when the photobioreactor is of the type where theprotective barrier forms a closely associated film or layer around thesolid support, a preferred orientation of the entire photobioreactor isvertical, but any orientation is acceptable. To be clear, theaforementioned orientations (e.g., vertical, horizontal, substantiallyvertical, non-horizontal, etc.) are relative to the floor or groundbeneath the cultivation support, assuming that the floor or ground ishorizontal.

Various structures, scaffolding, stands, racks, etc. may be used to holdor suspend a cultivation support or an entire photobioreactor in adesired orientation. In particular, the cultivation support and/or theprotective barrier can be suspended from, or attached to. a rope, line,hook, cable, track, rail, chain, shelf, pole, tube, scaffold, stand,beam or any other such structure capable of suspending the solidcultivation support and/or photobioreactor. Multiple cultivationsupports and/or photobioreactors may be suspended from a commonstructure, like sheets hanging from a clothes line. The cultivationsupport(s) and/or photobioreactor(s) may be suspended statically, or ina manner that allows for their movement. The position of the holes,loops, hooks, or the like will preferably distribute the weight of thecultivation support and/or photobioreactor substantially evenly.

Suspension of the photobioreactor or cultivation support, especially ina vertical orientation, is space efficient and may provide advantages inhandling. However, the bioreactor or cultivation support of theinvention need not be suspended. For example, in certain embodiments ofthe present invention, the cultivation support is sufficiently rigidthat if oriented non-horizontally, vertically, or substantiallyvertically (e.g., by securing or placing its base to/on a surface, in anembodiment in which the support is like a rigid plate, panel, grid,etc.) it can support its own weight and will remain so oriented. Inanother embodiment, the protective barrier is free standing, such as agreenhouse, and multiple cultivation supports are suspended and/orfree-standing within.

Suspension of the photobioreactor and/or cultivation support, especiallyin a vertical orientation, is space efficient and may provide advantagesin handling. However, the bioreactor or cultivation support of theinvention need not be suspended. For example, in certain embodiments ofthe present invention, the cultivation support is sufficiently rigidthat if oriented non-horizontally, vertically, or substantiallyvertically (e.g., by securing or placing its base to/on a surface, in anembodiment in which the support is like a rigid plate, panel, grid,etc.) it can support its own weight and will remain so oriented. Inanother embodiment, the protective barrier is free standing, such as agreenhouse, and multiple cultivation supports are suspended and/orfree-standing within.

Conveyance

Also described herein is a system for conveying photobioreactors,cultivation supports within the protective barrier of a photobioreactor,or some combination thereof from one location to another. The ability totransport a photobioreactor and/or cultivation support can beadvantageous for a variety of reasons. For example, it may allow foroptimizing their position(s) for receiving light, and for maintaining adesired temperature or gas content. The transportability can beparticularly advantageous when multiple photobioreactors or cultivationsupports are to be subject to discrete steps, such as inoculating,cultivating, inducing, and/or harvesting, because it is likely to bemore efficient to move the photobioreactors or cultivation supports toseveral assigned locations in a continuous-type process instead oftransporting the necessary materials and equipment to stationaryphotobioreactors or cultivation supports.

Thus, the growing surface, whether the cultivation support alone, or thecultivation support enclosed in a protective barrier, can be conveyed,even after inoculation. One of skill in the art will be familiar withnumerous types of conveyor systems frequently used in industrialapplications. The conveyance system is not limited to any particulartype so long as it is capable of moving one or more photobioreactors orcultivation supports. One skilled in the art will recognize that thetype of attachment between the photobioreactor or cultivation supportand the conveyor system will vary with the type of conveyance systememployed and will be selected to work cooperatively with any mountingpoints that are part of the cultivation support and/or the protectivebarrier. Although it is envisioned that the cultivation support(s) orphotobioreactor(s) will be conveyed in a mechanized manner powered byone or more motors (e.g., through the action of a chain and gears), itis also possible for them to be conveyed with human effort (e.g., bysimply pushing suspended bioreactors that are attached to a rail by abearing mechanism that slides along the rail).

A conveyor system that suspends photobioreactor(s) and/or cultivationsupport(s), especially in a vertical orientation, is space efficient andmay provide advantages in handling. But the conveyor system need notrely on suspending photobioreactor(s) or cultivation support(s). Forexample, a photobioreactor may move along on top of the conveyor system,such as by sliding over a roller conveyor. In one embodiment, theconveyor system may move photobioreactors comprising a cultivationsupport enclosed in a protective barrier. Alternatively, the protectivebarrier of a photobioreactor may be a large enclosure protecting one ormore conveyor systems moving multiple cultivation supports.

Photobioreactor Farm

For large scale applications, it may be impractical to construct asingle cultivation support of sufficient size. Thus is provided use oftwo or several or tens or hundreds or thousands or more cultivationsupports to cultivate photosynthetic microorganisms in a photobioreactor“farm.” These cultivation supports can all reside within a singleprotective barrier, thus comprising a single photobioreactor, ormultiple cultivation supports may be part of multiple photobioreactors.In either case, it can be beneficial to organize the multiplephotobioreactors or cultivation supports within a photobioreactor farmfor ease and efficiency of handling and processing. It can also bebeneficial to organize their arrangement to maximize the amount ofenergy captured from a light source such as the sun. Such organizationcan consist of arranging numerous photobioreactors or cultivationsupports in an orderly fashion such as, but not limited to, rows,columns, concentric circles, in grids, radiating outward from a centralpoint, and so forth.

In various embodiments, the farm comprises multiple photobioreactors orcultivation supports suspended from a common structure such as a track,rail, chain, line, or the like. In further embodiments, the structure ispart of a conveyor system and the photobioreactors or cultivationsupports move along the path of the conveyor system from one location toanother.

A photobioreactor farm can comprise one or an arrangement of multipleconveyor systems handling numerous photobioreactors or cultivationsupports. Such an arrangement could be scaled up to comprise two orseveral or tens or hundreds or thousands or more conveyor systemstogether handling two or several or tens or hundreds or thousands ormore photobioreactors or cultivation supports. In addition to theconveyor system(s), a photobioreactor farm can include defined areas,stations, or centers for performing steps such as inoculating,cultivating, inducing, and/or harvesting photosynthetic microorganisms.Such centers can be the location of specialized equipment for performingcertain steps. The paths of the conveyor systems can bring thephotobioreactors or cultivation supports to such centers where aparticular step is performed. The photobioreactor or cultivation supportcan then be moved along to the next area or center in the sequence.Different photobioreactors or cultivation supports along the conveyorsystem can reside at different centers along the path and thus besubject to different steps simultaneously. In one embodiment, the pathof the conveyor system is a loop. Once a photobioreactor or cultivationsupport completes one round of steps in the cultivation process, it canrepeat the process. Allowing for some units to be damaged or otherwiseeventually needing replacement, essentially the same set ofphotobioreactors or solid cultivation supports can be used repeatedly.

In a further embodiment, cultivation and harvest can occur at the sameor nearly the same location. This location is termed an inoculation andharvest center (see e.g., FIG. 3). Inoculation of the photobioreactorsand/or solid cultivation supports occurs at the inoculation and harvestcenter. The conveyor system forms a loop that then transports thephotobioreactors or cultivation supports away from the inoculation andharvest center. The photobioreactors or cultivation supports then travelalong the path of the conveyor system for an amount of time sufficientfor the desired amount of cell growth. The conveyor system then returnsthe photobioreactors or cultivation supports back to the inoculation andharvest center for harvest. Multiple conveyor systems can share a commoninoculation and harvest center from which they radiate out from. If evenmore capacity is needed, a photobioreactor farm can comprise multipleinoculation and harvest centers handling the photobioreactors orcultivation supports from multiple conveyor systems. Although increasedefficiencies may be realized, it is not necessary that the location ofinoculation and of harvest be the same or nearly the same location.

Methods of Using a Photobioreactor

Cultivation of Photosynthetic Microorganisms

A solid phase photobioreactor, as described herein, can be used forcultivating photosynthetic microorganisms. Photosynthetic microorganismsthat can be grown in the solid phase photobioreactor include, but arenot limited to, a naturally photosynthetic microorganism, such as acyanobacterium, or an engineered photosynthetic microorganism, such asan artificially photosynthetic bacterium. Exemplary microorgansims thatare either naturally photosynthetic or can be engineered to bephotosynthetic include, but are not limited to, bacteria; fungi;archaea; protists; microscopic plants, such as a green algae; andanimals such as plankton, planarian, and amoeba. Examples of naturallyoccurring photosynthetic microorganisms that can be grown in thebioreactor include, but are not limited to, Spirulina maximum, Spirulinaplatensis, Dunaliella salina, Botrycoccus braunii, Chlorella vulgaris,Chlorella pyrenoidosa, Serenastrum capricomutum, Scenedesmusauadricauda, Porphyridium cruentum, Scenedesmus acutus, Dunaliella sp.,Scenedesmus obliquus, Anabaenopsis, Aulosira, Cylindrospermum,Synechoccus sp., Synechocystis sp., and/or Tolypothrix.

Preferably, the photosynthetic microorganisms grown in the solid phasephotobioreactor comprise cyanobacteria. The cyanobacterium grown in thebioreactor can be any photosynthetic microorganism from the phylumCyanophyta. The cyanobacterium grown in the bioreactor can have aunicellular or colonial (e.g., filaments, sheets, or balls) morphology.Preferably, the cyanobacterium grown in the bioreactor is a unicellularcyanobacterium. Examples of cyanobacteria that can be grown in thebioreactor include, but are not limited to, the genus Synechocystis,Synechococcus, Thermosynechococcus, Nostoc, Prochlorococcu, Microcystis,Anabaena, Spirulina, and Gloeobacter. Preferably the cyanobacteriumgrown in the bioreactor is a Synechocystis spp. or Synechococcus spp.(e.g., Synechococcus elongatus PCC 7942 (ATCC 33912) and/orSynechocystis spp. PCC 6803 (ATCC 27184)). More preferably, thephotosynthetic microorganism grown in the bioreactor is a transgenicphotosynthetic microorganism engineered to accumulate a disaccharide, asdisclosed herein.

A solid cultivation support of a photobioreactor can be inoculated witha photosynthetic microorganism, along with addition of moisture andother components including, but not limited to, nutrients, salts,buffers, metals, nitrogen, phosphate, sulfur, etc. The photobioreactorcan then be releasably sealed with the cultivation support within theprotective barrier. The sealed photobioreactor can be placed, forexample by suspending it, in a location and manner to allow for controlof illumination and temperature. The placement can be static, or thephotobioreactor can be moved, such as to ensure maximum exposure to thesun's radiation over the course of a day. The photosyntheticmicroorganisms can be cultivated for a desired amount of time. One ofskill in the art will recognize that the length of time will varyaccording to the type of microorganism and the density of cell growthdesired. For example, for certain strains of cyanobacteria, acultivation period that is within the range of about four to about sevendays can provide a yield of cells that is within the range of about 50to about 250 grams of dry biomass per liter equivalent. Following aperiod for cultivation, the releasable seal can be opened and thephotosynthetic microorganisms can be harvested.

As used herein, “grams of dry biomass per liter equivalent” is a unitdetermined by calculating the average depth of the biomass layer (e.g.,about 150 microns) growing on the cultivation surface and multiplyingthat value by the length and the width of the cultivation surface. Thiscalculation provides a volume. The weight of the collected biomass fromthe cultivation surface can then be correlated to the volume andexpressed as “grams of dry biomass per liter equivalent.”

Method of Continuous Cultivation

Greater efficiencies can be realized if the process of cultivatingphotosynthetic microorganisms were to be made continuous, for example,like an assembly line. Instead of requiring the equipment and capacityto handle a large amount of biomass all at once that then sits idle inbetween batches, a continuous system would require less total capacity,but would utilize that capacity more efficiently through continuousoperation. By dividing cultivation into smaller but more numerouscomponents, the components can be organized in a spatially continuousarrangement. Different discrete steps of the overall production processcan then occur simultaneously. After a cultivation component issubjected to a process step, the component moves forward in the processwhile another component replaces it in that step. Therefore, productionof the end product would not be limited to the maturation of a largebatch, but can occur regularly as individual components complete theassembly line-like process. Further, following the completion of oneround of the process, the components can immediately start the processover and do so repeatedly.

More specifically, continuous cultivation relates to methods of usingconveyable photobioreactors or cultivation supports for cultivatingphotosynthetic microorganisms in a continuous manner. Continuous orcontinuous process is understood as the spatial relationship that canallow the photobioreactors or solid cultivation supports to progressfrom one step of the cultivation process to another. Alternatively, itis possible for a single large structural support to be utilized in acontinuous process. Specifically, the support can be a loop of material(e.g., terry cloth fabric) that is made to travel along a circuit (e.g.,like a conveyor belt that is arranged preferably vertically). The endresult is that biomass production can be achieved regularly as multiplephotobioreactors or solid cultivation supports finish the processsequentially and repeatedly. This type of process presents opportunitiesin large scale applications for increased efficiencies over producingbiomass in large, but infrequent batches.

In a preferred embodiment, the continuous spatial relationship is alongthe path of a conveyor system. The manner of operation is analogous toan assembly line. Such a conveyor system can operate in a number ofways. For example, the conveyor system can operate without interruptionwhile moving the photobioreactors or cultivation supports from onelocation to another. In such an embodiment, inoculation, harvesting, andthe like occur while the photobioreactors or cultivation supports are inmotion. Alternatively, the conveyor system can stop to allow for stepsto be performed, and then resume to move the photobioreactors orcultivation supports to the location of the next step. Further, theconveyor system can operate without interruption, and thephotobioreactors or cultivation supports can be detached from themovement of the conveyor system for processing, and then reattached tore-enter into the stream of conveyance. One skilled in the art willrealize that other permutations of this general theme are also possible.

In one embodiment of a method of continuous cultivation, multiplephotobioreactors are inoculated at one location along the conveyorsystem. The conveyor system then moves the photobioreactors to an areawhere cultivation of the photosynthetic microorganisms occurs. Duringthis portion of conveyance, the photobioreactors can be positioned toallow for optimal illumination to promote growth and photosynthesis.Next, the photobioreactors would arrive at a location where thephotosynthetic microorganisms can be harvested. The photobioreactors canthen return along the path of the conveyor system to the point ofinoculation to begin the process again. To improve efficiency, the timebetween when the photobioreactors leave the location of inoculation andarrive at the location of harvest can be made to coincide with the timeit takes for the desired amount of growth of the photosyntheticmicroorganisms to occur. The steps of the process are not limited toinoculation, cultivation, and harvest; additional steps can includeinducement of the cells to synthesize a desired product orsterilization. Although the above embodiment describes a system ofconveyable photobioreactors, it will be appreciated that the same typeof continuous cultivation can be practiced within a single protectivebarrier to convey and process multiple solid cultivation supports.

Method of Producing Fermentable Sugars

One technology that can benefit from the ability to more efficientlygrow photosynthetic microorganisms is the production of biomass foralternative fuels such as ethanol or biodiesel. Relative to plantscurrently grown to produce biomass such as corn, sugarcane, soybeans,canola, jatropha, and so forth, photosynthetic microorganisms, such ascyanobacteria, produce biomass at a much faster rate, which may lead tomuch greater productivity. In addition, direct production ofdisaccharides by microorganisms avoids much of the extensiveenergy-intensive pre-processing of using plant biomass to producefermentable sugar. Further, the use of phototrophic microorganismsinstead of plants can lead to higher yields of fermentable sugarswithout soil depletion, erosion, and diversion of the food supply.Relative to other microorganisms, preference is given to phototrophicmicroorganisms because their sources of carbon (CO₂) and energy (light)can be supplied from the environment, making them far less expensive tocultivate. In addition, phototrophic microorganisms can be utilized toconsume carbon emissions from industrial processes, thus providingfurther benefits to the environment.

One obstacle to producing high quantities of fermentable sugars fromphotosynthetic microorganisms is that they generally consume producedcarbohydrates rather than accumulating them. While some sugars, such assucrose or trehalose, are not utilized as a primary carbon source byphotosynthetic microorganisms, there are mechanisms for slowassimilation. In spite of reprocessing mechanisms, such material canaccumulate without being metabolized. If the organism is engineeredappropriately, the assimilation mechanism can be inactivated, whichenables high yields of sugars to be produced.

Provided herein is a method for producing fermentable sugars, especiallydisaccharide sugars, by photosynthetic microorganisms. Examples offermentable sugars include, but are not limited to, sucrose, trehalose,glucosylgycerol, and mannosylfructose. Preferably, the fermentable sugaris sucrose or trehalose. The method can be adapted to occur in acontinuous manner to improve the cost effectiveness of production.

Various embodiments of this method can be practiced using aphotosynthetic microorganism capable of synthesizing fermentable sugars.Some embodiments harness and control the natural phenomena of osmo- andmatric water protection for the generation of fermentation feedstocks.In one embodiment, synthesis of fermentable sugars is inducible. Inanother embodiment, synthesis of fermentable sugars can be modified bygenetic manipulation to be produced constitutively.

Fermentable sugar-producing photosynthetic microorganisms are preferablycyanobacteria. In some embodiments, a cyanobacterium accumulates adisaccharide according to inducible endogenous pathways. In someembodiments, a transgenic cyanobacterium accumulates a disaccharideaccording to engineered exogenous pathways. Both endogenous andexogenous pathways are discussed in further detail above.

Preferably, the transgenic photosynthetic microorganisms are one or moreof those discussed above.

Two non-limiting examples of strains of cyanobacteria capable ofaccumulating a disaccharide are Synechococcus elongatus PCC 7942 andSynechocystis sp. PCC 6803. Naturally occurring Synechococcus elongatusPCC 7942 synthesizes sucrose upon exposure to salt concentrations of upto about 700 mM, its tolerance limit. When glucosylglycerol biosynthesisis blocked by deletion of the agp gene, Synechocystis sp. PCC 6803produces sucrose as its osmoprotectant upon exposure to saltconcentrations up to its tolerance limit which may approach 900 mM. Insome embodiments, salt induction can be accomplished by introducingaerosolized saline solution applied directly to the cultivation surface.One advantage of this process is application can be controllablyintroduced along the growing surface depending on growth time of thecultivar thereby balancing accumulation of biomass and production of adisaccharide such as sucrose.

For producing fermentable sugars, the photosynthetic microorganisms canbe cultured and grown on a solid medium or in a liquid or gel medium.Culture and growth of photosynthetic microorganisms are well known inthe art. Except as otherwise noted herein, therefore, culture and growthof photosynthetic microorganisms can be carried out in accordance withsuch known processes. For example, a transgenic cyanobacteria engineeredto accumulate a disaccharide can be cultured and grown in a liquidmedium. The accumulated sugar can be isolated from such liquid medium ifexcreted from the cell. The accumulated sugar can be isolated fromphotosynthetic microorganisms harvested from the liquid medium. In oneembodiment, a transgenic cyanobacteria engineered to accumulatetrehalose, as discussed above, is cultured and grown in a liquid medium.Trehalose secreted from the transgenic cyanobacteria can be isolateddirectly from the liquid medium. In one embodiment, a transgeniccyanobacteria engineered to accumulate sucrose, as discussed above, iscultured and grown in a liquid medium. Sucrose can be isolated directlyfrom engineered cyanobacteria harvested from the liquid medium. In oneembodiment, a transgenic cyanobacteria engineered to accumulate andsecrete sucrose, as discussed above, is cultured and grown in a liquidmedium. Sucrose secreted from the transgenic cyanobacteria can beisolated directly from the liquid medium.

Preferably, photosynthetic microorganisms are cultivated to a relativelyhigh cell density of at least about 50 grams of dry biomass per literequivalent prior to induction. Such relatively high cell densities canbe achieved using a solid phase photobioreactor, as described herein.Disaccharide (e.g., sucrose) production can then be initiated/induced bytreating the accumulated biomass with defined concentrations of suitablesalt compounds effective at altering the activity of water in theculture media as measured by solution conductivity. In a furtherpreferred embodiment, sodium chloride is the salt used. Following anappropriate response time period (e.g., at least about 1 hour to nogreater than about 48 hours), the sucrose laden cells can be harvestedand processed to isolate and recover the sucrose produced. Typically, anappropriate response period is within the range of at least about 5hours to no greater than about 24 hours. More typically, the appropriateresponse period is within the range of at least about 10 hours to nogreater than about 20 hours.

In one embodiment, the majority of disaccharide (e.g., sucrose,trehalose, glucosylglycerol, mannosylfructose) synthesized accumulateswithin the cells. In another embodiment, the disaccharide is secreted bythe cells which can then be recovered from the photobioreactor.Regardless of whether the disaccharide is within the cells or secreted,the disaccharide can be obtained using any appropriate harvestingprocess including, but not limited to, an aqueous spray wash applied tothe cultivation surface. The wash comprising cells and/or disaccharidecan be collected and processed to isolate and recover the disaccharide.

Having described the invention in detail, it will be apparent thatmodifications, variations, and equivalent embodiments are possiblewithout departing the scope of the invention defined in the appendedclaims. Furthermore, it should be appreciated that all examples in thepresent disclosure are provided as non-limiting examples.

EXAMPLES

The following non-limiting examples are provided to further illustratethe present invention. It should be appreciated by those of skill in theart that the techniques disclosed in the examples that follow representapproaches the inventors have found function well in the practice of theinvention, and thus can be considered to constitute examples of modesfor its practice. However, those of skill in the art should, in light ofthe present disclosure, appreciate that many changes can be made in thespecific embodiments that are disclosed and still obtain a like orsimilar result without departing from the spirit and scope of theinvention.

Example 1 Solid Phase Photobioreactor

A static prototype device was constructed composed of a 2 milpolyethylene barrier layer with a Ziploc® resealable closure. A 60 sq.cm breathable panel was incorporated into one surface, and a 225 sq. cmwoven cotton fabric cultivation support surface was placed inside. Thedevice was sterilized by treatment with 70% volume aqueous ethanolfollowed by drying of the device at 50° C. with a stream of sterilefiltered air. 30 ml of sterile BG-11 culture media was absorbed onto thecultivation support followed by inoculation of the growing surface witha pre-culture of Synechococcus elongates PCC 7942. using an aerosolapplicator. The preculture was grown in BG-11 media at 26° C. for 2 daysprior to inoculation. The photobioreactor was placed in an incubationchamber maintained at 33° C. and illuminated at 300 microeinsteins withcool white fluorescent lamps. After 2 days, the reactor displayed activegrowth of organisms and was allowed to continue growth for an additional2 days whereupon the reactor was removed from the incubator and thegrowth surface washed with deionized water. The water was removed byevaporation to afford 254 mg dry weight biomass.

Example 2 Production of Sucrose by Photosynthetic Microorganisms

The following is a prophetic example to illustrate a method forproduction of sucrose by photosynthetic microorganism in combinationwith a photobioreactor. At least one photobioreactor, for example aphotobioreactor of the current invention such as described in Example 1or Example 3, may be run for approximately 4-7 days with eitherSynechocystis sp. PCC6803. or engineered Synechocystis sp. at atemperature range of between about 15 and 40° C., under illumination ofbetween about 60 and 300 microeinsteins, and carbon dioxideconcentration of between about 0.2 and 15 volume %. Following theinitial cultivation period the growth surface may be treated with anaqueous salt solution in the concentration range of between about 0.01and 1.5 M, more preferably between about 0.2 and 0.9 M, using an aerosolspray. The cultivation may be allowed to continue for approximately anadditional one to two days to allow sucrose production. The growthsurface may then be harvested by washing the surface with deionizedwater. In a further embodiment the wash water is sterile freshcultivation media and the washing stringency is such that between about70 and 90% of the cell mass is collected. The biomass remaining on thecultivation support may then be allowed to continue growth as asubsequent cycle. It is anticipated that the yield for thesecultivations should be between about 200 and 600 mg dry biomassdepending on the growth surface material and organism employed.

Example 3 Solid Cultivation Support Coated with an Absorbent Polymer

The growth surface of a static photobioreactor of the type described inExample 1 was prepared by dip coating the sterile dry surface of thematerial with a heated solution of sterile 1.5 weight percent agardispersed in BG-11 culture media. The coated growth surface was allowedto cool and harden upon which the surface was inserted into a sterilizedprotective barrier to form a photobioreactor device and inoculated withSynechococcus sp. grown in preculture as described in Example 1.Cultivation and harvesting were performed essentially as described inExample 1.

Example 4 ASF Gene Target

Biosynthesis of sucrose in cyanobacteria was explored through modulationof sucrose phosphate synthase (sps) and sucrose phosphate phosphatase(spp) activities. Such activities are already present in manycyanobacteria for acclimation to osmotic and matric water stress (seee.g., Lunn, J. E. 2002. Plant Physiol 128, 1490-1500). Lunn, J. E.(2002. Plant Physiol 128, 1490-1500) analyzed the genomic organizationof the sps and spp genes of several organisms, including Synechocystisspp. PCC 6803 and Synechococcus elongatus PCC 7942. Lunn proposed thatthe sucrose phosphate synthase (SPS) of Synechocystis spp. PCC 6803 (SEQID NO: 3) has an inactive sucrose phosphate phosphatase (SPP-like)domain and a distinct SPP activity. The SPP-like domain has a high levelof identity with the spp, but is missing many of the conserved activesite residues of the haloacid dehalogenase (HAD) superfamily. While nowork has yet been done on Synechococcus elongatus PCC 7942, Lunnproposed that both activities are contained within a single enzyme. Analignment of these enzymes is shown in FIG. 5.

Searches of the Synechococcus elongatus PCC 7942 genome did not reveal adistinct sps gene elsewhere on the chromosome. The Synechococcuselongatus PCC 7942 enzyme (SEQ ID NO: 2) was utilized so as to avoid thenecessity of multiple gene expression. While the gene from PCC 7942 hasbeen termed sps, because it is a single enzyme fusion bearing both SPSand SPP activities, it was termed asf for active SPS/SPP fusion (SEQ IDNO: 1) (see below for further information on the possible expression ofa distinct SPP enzyme.)

There are two approaches to expressing the Synechococcus elongatus PCC7942 asf gene product (SEQ ID NO: 2).

The first approach is a plasmid-based expression system built upon thebroad host range vector pMMB67EH (Furste, J. P., Pansegrau, W., Frank,R., Blocker, H., Scholz, P., Bagdasarian, M. and Lanka, E. 1986. Gene48, 119-131). Plasmid pMMB67EH is a derivative of RSF 1010, whichreplicates in most Gram-negative and even some Gram-positive organisms,thus allowing for plasmid-based analysis of sucrose production in E.coli, Synechocystis spp. PCC 6803, Synechococcus elongatus PCC 7942 anda variety of other cyanobacteria (Kreps, S., Ferino, F., Mosrin, C.,Gerits, J., Mergeay, M. and Thuriaux, P. 1990. Mol Gen Genet 221,129-133; Marraccini, P., Bulteau, S., Cassier-Chauvat, C.,Mermet-Bouvier, P. and Chauvat, F. 1993. Plant Molecular Biology 23,905-909; Gormley, E. P. and Davies, J. 1991. J Bacteriology 173,6705-8).

The second approach is stable integration into the chromosome ofSynechocystis spp. PCC 6803 and Synechococcus elongatus PCC 7942 at theupp (uracil phosphoribosyltransferase) locus. The upp locus was chosenfor reasons described below.

Example 5 Plasmid-Based Expression

Two plasmids were designed for plasmid-based expression of the asf geneproduct, pLybAL11 (see e.g., FIG. 6; SEQ ID NO: 19) and pLybAL12 (seee.g., FIG. 7; SEQ ID NO: 20). Plasmid pLybAL12 was constructed forexpression from predetermined promoters and pLybAL11 was constructed forexpression from promoters selected at random.

Both plasmids were constructed as follows. The asf gene fromSynechococcus elongatus PCC 7942 was amplified by PCR with theoligonucleotides 5′-AGACTACAATTGGGGCGTTTTCTGTGAG-3′ (the MfeIrestriction endonuclease site is nucleotide positions 7-12) (SEQ ID NO:7) and 5′-CTTACGTGCCGATCAACGTCTCATTCTGAAAAGGTTAAGCGATCGCCTC-3′ (SEQ IDNO: 8) using whole cells as the template, yielding the product of SEQ IDNO: 1.

The gene encoding for chloramphenicol acetytransferase (cat), both withand without the upstream promoter, was amplified from pBeloBAC11(GenBank Accession U51113).

The cat gene lacking the promoter was amplified from pBeloBAC11 by PCRwith the oligonucleotides 5′-TTATCGCGATCGTCAGGAGCTAAGGAAGCTAAAATGGAG-3′(SEQ ID NO: 9) and 5′-CGACCAATTCACGTGTTTGACAGCTTATC-3′ (SEQ ID NO: 10)(the PvuI and PmlI restriction endonuclease sites are at nucleotidepositions 4-9 and 10-15, respectively) to yield the product of SEQ IDNO: 11.

The cat gene bearing the promoter was amplified from pBeloBAC11 by PCRwith the oligonucleotides 5′-TTTTGGCGATCGTGAGACGTTGATCGGCACGTAAG-3′ (SEQID NO: 12) and 5′-CGACCAATTCACGTGTTTGACAGCTTATC-3′ (SEQ ID NO: 13) (thePvuI and PmlI restriction endonuclease sites are at nucleotide positions7-12 and 10-15, respectively) to yield the product of SEQ ID NO: 14.

The PCR products bearing the cat gene were digested with PvuI and theends blunted with T4 DNA polymerase. They were then individually ligatedto the asf PCR product. The resultant products were purified by agarosegel electrophoresis, digested with MfeI and PmlI and then ligated withT4 DNA ligase to the 6.6 Kbp product of pMMB67EH digested with EcoRI andHpaI. The ligation products were transformed into chemically competentNEB5α (New England Biolabs; Ipswich, Mass.) and selected for at 37° C.on LB agar supplemented with 100 m/ml ampicillin. Selected candidateswere grown at 37° C. in LB supplemented with 100 m/ml ampicillin forminiprep, analyzed by restriction endonuclease digest and then verifiedby sequence analysis with the oligonucleotides5′-GCTTCTGCGTTCTGATTTAATCTGTATCAG-3′ (SEQ ID NO: 15),5″-TATCACTTATTCAGGCGTAGCAACCAG-3′ (SEQ ID NO: 16),5′-GTCGTTAGTGACATCGACAACACACTG-3′ (SEQ ID NO: 17), and5′-GATCGCGATACTGATCGAGATAGGTC-3′ (SEQ ID NO: 18). Candidate number 5 ofpLybAL11 (pLybAL11-5) (SEQ ID NO: 19) and Candidate number 1 of pLybAL12(pLybAL12-1) (SEQ ID NO: 20) were chosen for further study.

Based upon plasmid yield during minipreps, it appears that the copynumber of these plasmids is greatly reduced when propagated in the E.coli strain NEB Turbo (New England Biolabs; Ipswich, Mass.), suggestingthe importance in choice of host strain for these plasmids.

Example 6 Promoter Insertion

Six promoters were chosen for insertion into pLybAL12-5. The presumedpromoter for Synechocystis spp. PCC 6803 carB encoding carbamoylphosphate synthase, which is likely to be immediately upstream of thegene pyrR where they would be co-transcribed as an operon, was chosenbecause it is likely to be strong due to its role in both pyrimidine andarginine biosynthesis. The nitrate reductase (nirA) promoters from bothSynechocystis spp. PCC 6803 (Aichi, M., Takatani, N. and Omata, T. 2001.J Bacteriol. 183, 5840-5847) and Synechococcus elongatus PCC 7942(Maeda, S-I. et al. 1998. J Bacteriol 180, 4080-4088) were chosen fortheir ability to be regulated by the source of nitrogen. The stronglight-phase promoter for the photosystem II D1 protein (psbAII) fromSynechococcus elongatus PCC 7942 (Golden, S. S., Brusslan, J. andHaselkorn, R. 1986. EMBO Journal 5, 2789-2798) and two dark-phasepromoters from Synechocystis spp. PCC 6803 [dnaK (Aoki, S., Kondo, T.and Ishiura M. 1995. J Bacteriol 177, 5606-11) and kaiA (Kucho, K-I. etal. 2005. J Bacteriol 187, 2190-2199)] were also selected as regulatedcyanobacterial derived promoters. Lastly, the λ_(PR)temperature-regulated promoter, which has been shown to be active incyanobacteria, was chosen (Fenno, F. and Chauvat, F. 1989. Gene 84,257-66; Mermet-Bouvier, P. and Chauvat, F. 1994. Current Microbiology28, 145-148).

The following oligonucleotides were used to amplify the promoters by PCRusing whole cells as the template, yielding the products shown. Therestriction endonuclease sites incorporated for cloning are provided inthe sequence.

Synechocystis spp. PCC 6803 pyrR (SphI/KpnI) (SEQ ID NO: 23) wasamplified from whole cells by PCR with the oligonucleotides5′-CGGTGTGCATGCCGTTATTGATGGAATG-3′ (SEQ ID NO: 21) and5′-TCACTAGGTACCTAAATTACCTGGGAAGCCAG-3′ (SEQ ID NO: 22), havingrestriction endonuclease sites at nucleotide positions 7-12 for both.

Synechocystis spp. PCC 6803 nirA (SphI/KpnI) (SEQ ID NO: 26) wasamplified from whole cells by PCR with the oligonucleotides5′-CCCAAGGCATGCAGGAAAACAAGCTCAGAATGCTG-3′ (SEQ ID NO: 24) and5′-TTTATTGGTACCAACGCTTCAAGCCAGATAACAGTAGAGATC-3′ (SEQ ID NO: 25), havingrestriction endonuclease sites at nucleotide positions 7-12 for both.

Synechococcus elongatus PCC 7942 psbAII (SphI/KpnI) (SEQ ID NO: 29) wasamplified from whole cells by PCR with the oligonucleotides5′-ATCTTTGCGTTCCGTGACGGCTACTG-3′ (SEQ ID NO: 27) and5′-GCAGATGGTACCGGTCAGCAGAGTG-3′ (having restriction endonuclease sitesat nucleotide positions 7-12) (SEQ ID NO: 28).

Synechococcus elongatus PCC 7942 nirA (SphI/KpnI) (SEQ ID NO: 32) wasamplified from whole cells by PCR with the oligonucleotides5′-CAGCCAGCATGCATAAATTTCTGTTTTGACCAAACCATCC-3′ (SEQ ID NO: 30) and5′-GTGGCTGGTACCATGGATTCATCTGCCTACAAAG-3′ (SEQ ID NO: 31), havingrestriction endonuclease sites at nucleotide positions 7-12 for both.

λ_(PR) (XbaI/KpnI) (SEQ ID NO: 35) was amplified from whole cells by PCRwith the oligonucleotides 5′-GTGCATTCTAGATGGCTACGAGGGCAGACAGTAAG-3′ (SEQID NO: 33) and 5′-TTCTGTGGTACCATATGGATCCTCCTTCTTAAGATGCAACCATTATCACC-3′(SEQ ID NO: 34), having restriction endonuclease sites at nucleotidepositions 7-12 for both.

Synechocystis spp. PCC 6803 dnaK (SphI/KpnI) (SEQ ID NO: 38) wasamplified from whole cells by PCR with the oligonucleotides5′-GCCCCAGCATGCACCAGTAAACATAAATCTC-3′ (SEQ ID NO: 36) and5′-ATTGGTGGTACCGAGGTCAATCCCAACAAC-3′ (SEQ ID NO: 37), having restrictionendonuclease sites at nucleotide positions 7-12 for both.

Synechocystis spp. PCC 6803 kiaA (SphI/KpnI) (SEQ ID NO: 41) wasamplified from whole cells by PCR with the oligonucleotides5′-GCCAGAGCATGCAAAGCTCACTAACTGG-3′ (SEQ ID NO: 39) and5′-GGAAAAGGTACCTGAGTCTATGGGCAACGTG-3′ (SEQ ID NO: 40), havingrestriction endonuclease sites at nucleotide positions 7-12 for both.

After amplification, the PCR products were digested with the restrictionendonucleases shown above, gel purified, and ligated into similarlydigested pLybAL12-1 to yield plasmids pLybAL15 (SEQ ID NO: 44), pLybAL16(SEQ ID NO: 45), pLybAL17 (SEQ ID NO: 46), pLybAL18 (SEQ ID NO: 47),pLybAL19 (SEQ ID NO: 48), pLybAL21 (SEQ ID NO: 49), and pLybAL21 (SEQ IDNO: 50), respectively. The ligation products were transformed intoelectrocompetent NEB5α (New England Biolabs; Ipswich, Mass.) andselected for at 30° C. on LB agar supplemented with 100 μg/mlampicillin, 34 μg/ml chloramphenicol, and 5% sucrose. Selectedcandidates were grown at 30° C. in LB supplemented with 100 m/mlampicillin, 34 μg/ml chloramphenicol and 5% sucrose for miniprep,analyzed by restriction endonuclease digest, and then verified bysequence analysis with the oligonucleotides5′-GCTTCTGCGTTCTGATTTAATCTGTATCAG-3′ (SEQ ID NO: 42) and5′-ATGGGTCTGAATGTGCAGAATGTAGAG-3′ (SEQ ID NO: 43). Candidates 6 and 7(pLybAL15-6 and pLybAL15-7), 2 (pLybAL16-2), 4 and 5 (pLybAL17-4 andpLybAL17-5), 1 and 2 (pLybAL18-1 and pLybAL18-2), 1 and 2 (pLybAL19-1and pLybAL19-2), 3 and 5 (pLybAL21-3 and pLybAL21-5) and 4 and 8(pLybAL22-4 and pLybAL22-8) were chosen for plasmids pLybAL15 (SEQ IDNO: 44), pLybAL16 (SEQ ID NO: 45), pLybAL17 (SEQ ID NO: 46), pLybAL18(SEQ ID NO: 47), pLybAL19 (SEQ ID NO: 48), pLybAL21 (SEQ ID NO: 49), andpLybAL21 (SEQ ID NO: 50), respectively.

Selection and growth of these plasmids on LB supplemented with sucroseand both antibiotics was essential to obtaining clones. Selection wasoriginally conducted on LB supplemented with ampicillin alone, butplasmids containing a promoter could not be isolated. Isolates wereeither re-ligation of the vector alone or of varying size and lackingthe ability to be propagated in the presence chloramphenicol. It isthought that internal sucrose was being produced, creating an osmoticshock for the cells that leads to deletions preventing sucroseproduction. Subsequent experiments indicated that, once isolated, theplasmids may be stable in the absence of sucrose, possibly through theeventual induction of osmotic stress machinery and/or sucroseconsumption enzymes.

Example 7 Transformation of Synechocystis and Synechococcus

The promoter-containing plasmids, pLybAL15 (SEQ ID NO: 44), pLybAL16(SEQ ID NO: 45), pLybAL17 (SEQ ID NO: 46), pLybAL18 (SEQ ID NO: 47),pLybAL19 (SEQ ID NO: 48), pLybAL21 (SEQ ID NO: 49), and pLybAL21 (SEQ IDNO: 50), as well as the promoterless pLybAL12-1 vector (SEQ ID NO: 20)(see Examples 5-6), were placed into both Synechocystis spp. PCC 6803and Synechococcus elongatus PCC 7942 by triparental conjugation,performed consistent with Elhai, J. and Wolk, C. P. 1988. Methods inEnzymology 167, 747-754, unless indicated otherewise.

Overnight cultures of the cargo strains (NEB5α bearing the plasmids tobe transferred), as well as an overnight culture of HB 101 bearing thehelper plasmid pRK2013 (ATCC 37159) grown at 30° C. were pelleted bycentrifugation, washed twice with LB and then resuspended in LB inone-tenth the original volume. Each cyanobacterium was grown at 30° C.in BG11-A, which is the same as BG11 except the trace elements have beenreplaced with Nitsch's trace elements (Nitsch, J. P. and Nitsch, C.1956. American Journal of Botany 43, 839-851) under constantillumination to an OD₇₃₀ of approximately 0.5. The cells were pelletedby centrifugation, washed twice with BG11-A, and resuspended in BG11-Awith a 7.5-fold increase in concentration. A series of 10-fold dilutionsof the cyanobacteria in BG11-A were prepared down to 10⁻⁵. At eachdilution, 100 μl of the cyanobacterium was combined with 50 μl each ofthe cargo and helper strains of E. coli. 150 μl of each mixture was thenplated onto BG11-A agar (1.5%) plates supplemented with 5% LB. Theplates were incubated at 26-28° C. under constant illumination for 16 to24 hours. The agar (app. 30 ml) on each plate was lifted and 300 μl of a100× chloramphenicol solution was added. The final concentration ofchloramphenicol was 25 μg/ml for Synechocystis spp. PCC 6803 and 7.5μg/ml for Synechococcus elongatus PCC 7942. Incubation continued for8-12 days. Individual colonies of transconjugants were purified awayfrom contaminating E. coli by restreaking onto BG11-A supplemented withthe appropriate amount of chloramphenicol to, again, obtain isolatedcolonies.

Example 8 Promoter Library in pLybAL11-5

The following example describes construction of a library ofcyanobacterial DNA for promoter selection using pLybAL11-5 (SEQ ID NO:19) (see Example 5). A modified, scaled up version of the chromosomalDNA isolation protocol of Wilson, K. (1997. Preparation of Genomic DNAfrom Bacteria. In Current Protocols in Molecular Biology. John Wiley andSons Vol. 1, pp. 2.4.1-2.4.5) was employed, where the primarydifferences were much longer incubation times and the replacement of SDSwith Sarkosyl. The DNA isolated was of sufficient quality for partialSau3AI digest for insertion into the BamHI site of pLybAL11-5. As shownin FIG. 8, some of the fragments would have promoters and others wouldnot.

During the process of library construction, a possible promoter withinthe asf gene was discovered. To function as a promoter cloning vector,plasmid pLybAL11-5 (SEQ ID NO: 19) is supposed to only be resistant tochloramphenicol when a promoter has been inserted in front of the asfgene, as the marker lacks its normal promoter and the promoter upstreamof asf was not included. Once constructed, however, the chloramphenicolresistance conferred by this plasmid was examined in E. coli. When NEB5αbearing pLybAL11-5 was cultured on LB agar (1.5%) supplemented with 34μg/ml chloramphenicol at 37° C., growth was observed. When cultured inliquid LB medium supplemented with 34 μg/ml chloramphenicol, however,little-to-no growth was observed. NEB5α bearing pLybAL12-1 (SEQ ID NO:20) grows in the presence of chloramphenicol on both solid and in liquidLB medium.

To verify there was no missed promoter upstream of the asf gene butdownstream of the transcription terminators, the insert placed intopMMB67EH to make pLybAL11 was cloned into Lucigen Corp.'s (Middleton,Wis.) pSMART-LCKan blunt-end cloning vector using Lucigen's CloneSmartkit with the Lucigen strain of E. coli (E. cloni 10G) competent cells(see e.g., FIG. 9). Because it was blunt-ended cloning, the insertscould ligate to the plasmid in either direction to create pLybAL13f (SEQID NO: 51) and pLyAL13r (SEQ ID NO: 52). This vector is specificallydesigned to eliminate transcription read through from the vector bysurrounding the cloning site with terminators. As a control, the insertused to construct pLybAL12 was also placed into this vector, creatingpLybAL14f (SEQ ID NO: 53) and pLybAL14r (SEQ ID NO: 54). The plasmidslooked to be the appropriate size on an agarose gel but inserts were notverified by DNA sequencing to confirm the integrity of the clones.Similar results, however, were seen for E. cloni 10G bearing pLybAL13and pLybAL14 (with the cloned DNA ligated in either direction for r) aswere seen for NEB5α bearing pLybAL11 (SEQ ID NO: 19) and pLybAL12 (SEQID NO: 20), respectively. This indicates that the activity of thispromoter is weak in E. coli.

Many E. coli promoters do not function in cyanobacteria, and vice versa.It is possible that this promoter activity would not be observed inSynechocystis spp. PCC 6803 or Synechococcus elongatus PCC 7942. Tocheck this, pLybAL11-5 (SEQ ID NO: 19) was inserted into both organismsby conjugation, as described above. On BG11-A agar (1.5%) supplementedwith chloramphenicol (25 μg/ml and 7.5 μg/ml for Synechocystis spp. PCC6803 and Synechococcus elongatus PCC 7942, respectively), growth wasobserved.

Growth of these organisms bearing pLybAL11-5 (SEQ ID NO: 19) on liquidBG11-A supplemented with chloramphenicol was examined. It is possiblethat this activity is very weak and is only observable when present on amultiple-copy plasmid. This may be the case with E. coli, but is notlikely with the cyanobacteria. RSF1010 is a relatively low-copy plasmid,having only 12 copies in E. coli (Frey, J., Bagdasarian, M. M. andBagdasarian, M. 1992). Gene 113,101-106). E. coli undergoing rapiddivision has at most 2 copies of its chromosome, thus at least a 6-foldincrease in copy number. A comparable copy number in cyanobacteria forthis plasmid is likely. The chromosomal copy numbers of Synechocystisspp. PCC 6803 and Synechococcus elongatus PCC 7942 of 10-12 and 16,respectively, are similar (Labarre, J., Chauvat, F. and Thuriaux, P.1989. J Bacteriol 171, 3449-57). The results above suggest the presenceof a promoter within the asf gene of cyanobacteria.

FIG. 10 shows a possible location of a promoter (or promoters) withinthe asf gene. Transcription initiation elements have been described byCurtis, S. E. [1994. The transcription apparatus and the regulation oftranscription initiation. In The Molecular Biology of Cyanobacteria.Bryant, D. A. (ed). Kluwer Academic Publishers pp. 613-699]. Translationinitiation elements have been defined by Sazuka, T. and Ohara, O. (1996.DNA Research 3, 225-232).

Based upon alignment to known SPS enzymes and the presence of a stopcodon only two codons upstream, the translation initiation of the asfgene is predicted to start at a GTG start codon. While ATG start codonsare the most common, GTG and TTG are less common, but not rare. Atypical E. coli-like Shine-Delgarno sequence (GGAG or GAGG)complementary the 3′-end of the 16S rRNA for which the adeninenucleotide is optimally 9-12 by away from the first nucleotide of thestart codon is also present, except with somewhat longer spacing. Thissequence is found in about half the genes studied by Sazuka and Ohara.Less optimal spacing is not uncommon, but often leads to reduced levelsof expression. There is too little sequence upstream of theShine-Delgarno sequence but downstream of the MfeI site to incorporate apromoter. It is possible that a partial promoter may be incorporated,but the rest of the promoter would have to produced by the vectorsequence of all three plasmids (pLybAL11-5 (SEQ ID NO: 19); pLybAL13f(SEQ ID NO: 51); and pLybAL13r (SEQ ID NO: 52)), which is improbable.

Thus it likely that the promoter activity is located within the asfgene. If the promoter is within the asf gene, one potential position isin front of the SPP domain of asf. This would give the sucrosebiosynthetic enzymes of Synechococcus elongatus PCC 7942 a similarquaternary structure to those from Synechocystis spp. PCC 6803. Eachorganism would have two proteins, an SPS domain with a translationallyfused SPP or SPP-like domain and a distinct SPP that may (or may not)interact with each other.

First, it was determined whether the SPP domain of asf could even betranslated separately. As can be seen in FIG. 10 and Table 1, there is aTTG start codon immediately upstream of the SPP domain that is precededby a Shine-Delgarno sequence.

TABLE 1 Nucleotides immediately surrounding the proposed spp startcodon. The nucleotides immediately surrounding the proposed spp startcodon are compared to the consensus of 72 cyanobacterial genes.Nucleotides matching the consensus are italicized, whereas nucleotidesthat do not match the consensus are underlined. Nucleotide numbers arerelative to the first nucleotide of the start codon. NT# −10 −9 −8 −7 −6−5 −4 −3 −2 −1 123 4 5 6 Consensus A/G A/G A/T A/T A/T A/T A/T A/T C/TT/C ATG A/G C C/T Selo7942 asf T G A C T A G C G C GTG G C A Selo7942spp T C G C A A A C G C TTG A T T

The region surrounding the start codon matches the consensus determinedby Sazuka and Ohara for 72 cyanobacterial genes almost as well as thenative start codon. While determining cyanobacterial promoters basedupon rules established for E. coli promoters, the typical −35 and −10elements were searched for since the promoter does appear to be activein E. coli. Two possible promoters were identified, as seen in FIG. 10.There remains the possibility of an additional promoter(s) elsewhere inasf.

Example 9 Transfer of Plasmids from E. Coli to Cyanobacteria

Conjugation was used for transfer of the pMMB67EH-based plasmids intocyanobacteria. Protocols exist for the transformation of these organisms(Zang, X., Liu, B., Liu, S., Arunakumara, K. K. I. U. and Zhang, X.2007. Journal of Microbiology 45, 241-245; Golden, S. S. and Sherman, L.A.1984. Journal of Bacteriology 158, 36-42), but such approaches wereunsuccessful for placing these plasmids into Synechocystis spp. PCC 6803and Synechococcus elongatus PCC 7942 using natural transformation.

The presence of the plasmids in the cyanobacteria was verified.Transconjugants were analyzed for the presence of plasmid by PCR of theasf/cat gene combination with the oligonucleotides5′-AGACTACAATTGGGGCGTTTTCTGTGAG-3′ (SEQ ID NO: 7) and5′-GGTGGTTGTGTTTGACAGCTTATC-3′ (SEQ ID NO: 55), yielding a 3.1 kbproduct. In addition, plasmids were isolated and analyzed. Cultures ofcells grown in BG11-A supplemented with chloramphenicol (at theconcentrations described above) are pelleted by centrifugation,resuspended in TE, heat-treated and miniprepped by the Promega Wizard SVPlus miniprep kit. But with poor yield, direct plasmid analysis isdifficult. As such, the isolated DNA is transformed into E. coli NEB5α,re-isolated using the Promega Wizard SV Plus miniprep kit, and thensubjected to restriction endonuclease analysis.

Example 10 Sucrose Production Assay and Analysis

Synechococcus transformed with pLybAL19 or pLybAL17 (see Example 7) wasassayed for sucrose accumulation. Sucrose is measured with BioVision,Inc.'s (Mountain View, Calif.) sucrose assay kit. Assays were runfollowing a 4 hour induction period (increased light to 180microeinsteins from 50 microeinsteins for pLybAL17 (SEQ ID NO: 46) andincreased temperature from 26 to 39° C. for pLybAL19 (SEQ ID NO: 48)).Data was corrected for background glucose present in the cells.

Results showed Synechococcus transformed with pLybAL19 (SEQ ID NO: 48)accumulated 0.78 nanomoles of sucrose per mg of dry biomass. Resultsalso showed that Synechococcus transformed with pLybAL17 (SEQ ID NO: 46)accumulated 0.95 nanomoles of sucrose per mg of dry biomass.

Further analysis for plasmid-based sucrose production in E. coli,Synechocystis spp. PCC 6803, and Synechococcus elongatus PCC 7942 wasperformed. Because bacteria can consume sucrose, detection may bedifficult. As such, cells are grown under suppressing conditions andthen assayed shortly after induction. The pyrR promoter may besuppressed by growth with uracil and induced by transfer medium lackinguracil. The nirA promoters can be suppressed by growth with ammoniumions as the nitrogen source and induced by transfer to medium withnitrate as the nitrogen source. The psbAII promoter can be shifted fromlow light to high light. The dark phase promoters can be shifted fromlight to dark. And, the λ_(PR) promoter can be shifted from low (25° C.)to high (39° C.) temperature.

Example 11 Expression Through Stable Chromosomal Integration

Insertion of sucrose biosynthetic genes can cause a negative impact oncell growth, leading to difficulties in obtaining complete segregationof the 10-16 chromosomes. With normal selection for an antibioticresistance marker, having additional copies of the marker does notdramatically impact the cells ability to survive in the presence ofantibiotic. Therefore, complete chromosomal segregation can be difficultto achieve using antibiotic selection when faced with a negativephenotype.

Deletion of the upp gene (encoding for uracil phosphoribosyltransferase)in most organisms leads to resistance to the otherwise toxic5-fluorouracil. To obtain complete resistance, all copies of the uppgene must be deleted. Thus integrating into the upp locus ofSynechocystis spp. PCC 6803 (SEQ ID NO: 56) and Synechococcus elongatusPCC 7942 (SEQ ID NO: 58) will lead to 5-fluorouracil resistance andallow for positive selection of complete segregation, even in thepresence of a negative phenotype.

Example 12 The Upp/Kanamycin Resistance Cassette

A general strategy for genomic manipulation using a upp/kanamycinresistance cassette is outlined in FIG. 11. Deletion of a gene isdepicted, but the strategy can easily be modified at the “replacement”step for insertions and mutations.

An upp/kanamycin resistance cassette was constructed. The cassette wasconstructed in Epicentre Biotechnologies CopyControl cloning kit withblunt-end cloning vector pCC1 and E. coli strain EPI300 according tomanufacturer protocols. The upp gene from Bacillus subtilis 168 wasamplified from whole cells using the oligonucleotides5′-AAGAAGCAAGACAGCGTGTAGCTGCTCTGACTG-3 (SEQ ID NO: 60) and5′-TCCCGGGATTTGGTACCTTATTTTGTTCCAAACATGCGGTCACCCGCATC-3′ (havingrestriction endonuclease sites at nucleotide positions 2-7 and 12-17)(SEQ ID NO: 61), yielding the product of SEQ ID NO: 62.

The PCR product was cloned into pCC1 and those bearing the insert wereselected for on LB supplemented with chloramphenicol as described inEpicentre

Biotechnologies' protocol. The forward orientation, relative to lacZ,was screened for by restriction endonuclease digest, yielding pLybAL7f(SEQ ID NO: 65). The exact sequence of the insert was verified by DNAsequencing with the oligonucleotides 5′-GTAATACGACTCACTATAGGGC-3′ (SEQID NO: 63) and 5′-CACACAGGAAACAGCTATGACCAT-3′ (SEQ ID NO: 64) forcandidates 3 and 8 (pLybAL7-3 and pLybAL7-8).

The kanamycin resistance marker from the Lybradyn vector pLybAA1[originally derived from pACYC177 (Rose, R. E. 1988. Nucleic Acids Res.16, 356] was amplified with the oligonucleotides5′-GTCAGTGCACTGCTCTGCCAGTGTTACAACC-3′ (having ApaLI restrictionendonuclease sites at nucleotide positions 5-10) (SEQ ID NO:

66) and 5′-CTCAGTGGCGCCAAAACTCACGTTAAGGGATTTTGGTC-3′ (SEQ ID NO: 67)(having NarI restriction endonuclease sites at nucleotide positions7-12), yielding the product of SEQ ID NO: 68.

The PCR product was digested with ApaLI and NarI and ligated intosimilarly digested pLybAL7f, creating pLybAL8f (SEQ ID NO: 69). Theproper plasmid was selected for on LB supplemented with 50 μg/mlneomycin and examined by restriction endonuclease digestion.

Example 13 Upp Deletion

One strategy to force segregation of chromosomal inserts for theexpression of sugars, including sucrose, trehalose, glucosylglycerol,and mannosylfructose, utilizes deletion of upp from the chromosomeleading to resistance to 5-fluorouracil. While this has been establishedin many organisms (such as E. coli and B. subtilis), it has notpreviously been established for cyanobacteria, such as Synechocystisspp. PCC 6803 and Synechococcus elongatus PCC 7942.

Testing showed that growth of each of these organisms was completelyinhibited by 1 μg/ml, 5-fluorouracil. Growth of Synechocystis spp. PCC6803 is completely inhibited by 0.5 μg/ml, 5-fluorouracil and issensitive to as little as little as 0.1 μg/ml, 5-fluorouracil.

The upp gene and surrounding sequences of both Synechocystis spp. PCC6803 was amplified with the oligonucleotides Sspupp-F (SEQ ID NO: 96)and Sspupp-R (SEQ ID NO: 97). The upp gene and surrounding sequences ofSynechococcus elongatus PCC 7942 was amplified with the oligonucleotidesSeloupp-F (SEQ ID NO: 98) and Seloupp-R (SEQ ID NO: 99). The PCRproducts (upp of Synechocystis spp. PCC 6803, SEQ ID NO: 100; upp ofSynechococcus elongatus PCC 7942, SEQ ID NO: 101) were then cloned intothe Epicentre Biotechnologies' (Madison, Wis.) blunt cloning vectorpCC1, as per the manufacturer's instructions.

While the PCR product (SEQ ID NO: 100 or SEQ ID NO: 101) can ligate intopCC1 in either direction, the forward orientation relative to the lacpromoter was chosen, generating pLybAL3f (SEQ ID NO: 102) (containingupp of Synechocystis spp. PCC 6803) and pLybAL5f (SEQ ID NO: 103)(containing upp of Synechococcus elongatus PCC 7942), respectively. Theinserts were sequenced using oligonucleotides T7long (SEQ ID NO: 104)and M13rev (SEQ ID NO: 105). The nucleotide sequence of upp ofSynechocystis spp. PCC 6803 is represented by SEQ ID NO: 111 and thepolypeptide sequence by SEQ ID NO: 112. The nucleotide sequence of uppof Synechococcus elongatus PCC 7942 is represented by SEQ ID NO: 113 andthe polypeptide sequence by SEQ ID NO: 114.

Plasmid pLybAL4f (SEQ ID NO: 106) was created from pLybAL3f (SEQ ID NO:102) by removal of the BlpI and ApaLI fragment, blunt ending with T4 DNApolymerase and then recircularizing with T4 DNA ligase. Part of theSynechocystis spp. PCC 6803 upp gene was then deleted by digestingpLybAL4f with AvrII and SgfI, blunt ending with T4 DNA polymerase andthen recircularizing with T4 DNA ligase, creating pLybAL9f (SEQ ID NO:107). The SacI/SphI fragment (SEQ ID NO: 108) bearing the cyanobacterialDNA was excised from pLybAL9f (SEQ ID NO: 107) and ligated intosimilarly digested pAR0180 (sequence not completely known; Parke, D.1990. Construction of mobilizable vectors derived from plasmids RP4,pUC18 and pUC19. Gene 93:135-137; ATCC 77123), creating pLybAL25.Plasmid pLybAL6fb (SEQ ID NO: 109) was created from pLybAL5f by removalof the SapI and ApaLI fragment, blunt ending with T4 DNA polymerase andthen recircularizing with T4 DNA ligase. Part of the Synechococcuselongatus PCC 7942 upp gene was then deleted by digesting pLybAL6fb withBssHII and BsaI, blunt ending with T4 DNA polymerase and thenrecircularizing with T4 DNA ligase, creating pLybAL10fb (SEQ ID NO:110). The SacI/SphI fragment (SEQ ID NO: 138) bearing the cyanobacterialDNA was excised from pLybAL10fb and ligated into similarly digestedpAR0180, creating pLybAL26.

Plasmids pLybAL25 and pLybAL26 were placed in E. coli 517-1 (ATCC47055). Plasmids pLybAL25 and pLybAL26 are to be transferred toSynechocystis spp. PCC 6803 and Synechococcus elongatus PCC 7942 bybiparental conjugation. Since these plasmids do not replicate incyanobacteria, they should function as suicide vectors and cross overinto the chromosome, deleting upp on one of the copies of thechromosome. An optimized protocol will enable speeding of segregationwithout killing the cells by premature exposure to too much5-fluorouracil.

Example 14 Modification Of Sucrose Degradation Enzymes

Cyanobacteria transformed with asf are further engineered to improvesucrose production by modulation of sucrose degradation activity.

The inventors have identified genes encoding invertase homologues inboth Synechocystis spp. PCC 6803 (nucleotide sequence SEQ ID NO: 70;polypeptide sequence SEQ ID NO: 71) and Synechococcus elongatus PCC 7942(nucleotide sequence SEQ ID NO: 72; polypeptide sequence SEQ ID NO: 73).Synechocystis spp. PCC 6803 also encodes a sucraseferredoxin-likeprotein (nucleotide sequence SEQ ID NO: 74; polypeptide sequence SEQ IDNO: 75) (Machray G. C. et al. 1994. FEBS Lett 354, 123-127).

These genes are deleted using the markerless deletion protocol describedin FIG. 11.

Example 15 Modification of Sucrose Degradation Enzymes

Cyanobacteria transformed with asf are further engineered to promotesucrose secretion from the cells.

When in a low osmotic environment, the sucrose may be automaticallyexpunged from the cells, as done with osomoprotectants by some organismswhen transitioning from high to low salt environments (Schleyer, M.,Schmidt, R. and Bakker, E. P. 1993. Arch Microbiol 160, 424-43; Koo, S.P., Higgins, C. F. and Booth, I. R. 1991. J Gen Microbiol 137,2617-2625; Lamark, T., Styrvold, O. B. and Strgim, A. R. 1992. FEMSMicrobiol. Lett 96, 149-154). Engineering of cyanobacteria can promotesuch a process.

Cyanobacteria transformed with asf are further engineered to expresssucrose permease, such as those used by E. coli and Salmonella or in thetransport of sucrose to nitrogen-fixing cysts of certain cyanobacteria(Jahreis K. et al. 2002. J Bacteriol 184, 5307-5316; Cumino, A. C. 2007.Plant Physiol 143, 1385-97). These genes are cloned and transformed intocyanobacteria according to techniques described above.

Example 16 Sucrose Secretion by Cyanobacteria Transformed with Porin

Sucrose secretion from Synechocystis spp. PCC 6803 and Synechococcuselongatus PCC 7942 can be facilitated by transformation with sucroseporin.

The gene encoding sucrose porin (scrY) from Enterobacter sakazakii ATCCBAA-894 was cloned for expression in Synechocystis spp. PCC 6803 andSynechococcus elongatus PCC 7942. The function of this gene has beeninferred from its sequence and those of its neighbors. Enterobactersakazakii scrY was amplified from chromosomal DNA by PCR with theoligonucleotides EsscrYBamHI-F (SEQ ID NO: 88) and EsscrYSacI-R (SEQ IDNO: 89). The PCR product (SEQ ID NO: 90) was digested with BamHI andSacI and ligated into similarly digested pLybAL19 and cloned into NEB5α,creating pLybAL32 (SEQ ID NO: 91). The scrY gene (nucleic acid SEQ IDNO: 94; polypeptide sequence, SEQ ID NO: 95) was then sequenced with theoligonucleotides EsscrYmidseq-F (SEQ ID NO: 92) and EsscrYmidseq-R (SEQID NO: 93). When introduced into the host, this construct allows for theco-expression of the genes scrY and asf under the control of thetemperature-inducible promoter. This plasmid was transferred bytri-parental conjugation (as described above) into Synechocystis spp.PCC 6803. The transformed Synechocystis spp. PCC 6803 is tested forefficacy in the secretion of sucrose. Similar transformation and testingof Synechococcus elongatus PCC 7942 follows.

Example 17 Generation of Trehalose a Accumulating Cyanobacteria

The trehalose biosynthetic genes encoding trehalose phosphate synthaseand trehalose phosphate phosphatase (otsA and otsB, respectively) fromE. coli are found in a two gene operon, otsBA (SEQ ID NO: 115). Theoperon was cloned by PCR amplification of E. coli K12 genomic DNA withthe oligonucleotides EcotsBA-F (SEQ ID NO: 116) and EcotsBA-R (SEQ IDNO: 117). The PCR product was digested with AflII and NheI and wascloned into pLybAL19 (SEQ ID NO: 48), replacing most of the asf gene.The new plasmid, pLybAL23 (SEQ ID NO: 118), places the trehalosebiosynthetic genes under the control of the temperature-inducible λ_(PR)promoter. The genes were sequenced to verify their integrity with theoligonucleotides EcotsBAmidseq-F (SEQ ID NO: 119) and EcotsBAmidseq-R(SEQ ID NO: 120). Expression of the otsBA operon was then placed undercontrol of the pyrR, psbAII, dnaK and kiaA promoters (as describedabove) by ligating the AflII (blunt-ended with T4 DNA polymerase)/NheIfragment of pLybAL23 bearing the otsBA operon, into pLybAL15, pLybAL17,pLybAL21 and pLybAL22 digested with SacI (blunt-ended with T4 DNApolymerase) and NheI, creating pLybAL28 (SEQ ID NO: 121), pLybAL29 (SEQID NO: 122), pLybAL30 (SEQ ID NO: 123), and pLybAL31 (SEQ ID NO: 124),respectively.

Each of plasmids pLybAL28 (SEQ ID NO: 121), pLybAL29 (SEQ ID NO:

122), pLybAL30 (SEQ ID NO: 123), and pLybAL31 (SEQ ID NO: 124) weremoved into Synechocystis spp. PCC 6803 by tri-parental conjugation (asdescribed above).

Expression of the otsBA operon from pLybAL23 was placed under thecontrol of the Synechocystis spp. PCC 6803 and Synechococcus elongatusPCC 7942 nirA promoters (as described above) in pLybAL16 and pLybAL18 inthe same way as just described for the other promoters, creatingpLybAL36 (SEQ ID NO: 125) and pLybAL37 (SEQ ID NO: 126), respectively.

Example 18 Trehalose Assay

Biomass was separated from the culture broth as necessary bycentrifugation and residual biomass was removed from the clarifiedculture broth by filtration through 0.2 micron filter. The culture brothwas concentrated to a residue by evaporation under reduced pressure. Theconcentrated culture broth was dissolved in 1 ml of de-ionized water andthen 10 microliters of solution was sampled in a trehalose assay. Thebiomass collected by centrifugation was transferred to a weigh dish andheated to 100° C. to remove residual moisture. The dry biomass wasweighed and then a 100 mg sample was dissolved in 1 ml of de-ionizedwater. The mixture was then ground and the solids were removed bycentrifugation. A 10 microliter sample of the clarified supernatant wasdiluted 100 fold with de-ionized water and 10 microliters of the dilutedsample were tested for trehalose.

The assay for trehalose used a modified procedure of a commerciallysupplied sucrose assay kit available through Biovision, Inc. Themodification to the standard protocol was the substitution of trehalasefor the kit supplied invertase enzyme solution. The kit involves thehydrolysis of trehalose with trehalase to release glucose. The glucoseis oxidized by glucose oxidase to produce hydrogen peroxide which isdetected by the action of peroxidase in the presence of a coloredindicator. The colored indicator is quantitatively measured by itscharacteristic absorbance at 570 nm to afford the concentration ofglucose originally present in the sample.

Trehalase (treA nucleic acid SEQ ID NO: 134 encoding trehalasepolypeptide SEQ ID NO: 135) was prepared from the recombinant E. colitreA gene which has been engineered into a plasmid and transformed intoan E. coli host by a similar method as described by Gutierrez C,Ardourel M, Bremer E, Middendorf A, Boos W, Ehmann U. Mol Gen Genet.1989 June; 217(2-3):347-54. Periplasmic trehalase was cloned from E.coli K12, encoded by treA. The treA PCR product (SEQ ID NO: 127) wasdigested with AflII/XbaI and then ligated into similarly digestedpLybCB6, a proprietary plasmid with a constitutive version of the strongE. coli trp promoter, creating pLybAL24 (SEQ ID NO: 130). The integrityof the insert was analyzed by sequencing with the oligonucleotidesEctreAmidseq-F and EctreAmidseq-R.

A C-terminal His₆-tagged version of the trehalase was constructed. Thegene was amplified by PCR with the oligonucleotides EctreA-F2 (SEQ IDNO: 131) and EctreA-R2 (SEQ ID NO: 132). The PCR product (SEQ ID NO:136) was then digested with AfiI/XbaI and then ligated into similarlydigested pLybAL24, creating pLybAL33 (SEQ ID NO: 133).

Strong constitutive expression of the periplasmic trehalase isdetrimental to the cells, causing a strong growth defect at 37° C. Thiscan be significantly alleviated by growing the cells at 30° C.

The protein was expressed in E. coli BW25113 on a plasmid pLYBAL24 (SEQID NO: 130) which was grown in 2×YT media containing kanamycin. Theprotein was produced constitutively using the Trp promoter and containsa signal peptide which allows the protein to be transported to theperiplasm. Following fermentation and harvesting of the biomass, theenzyme was purified by selective periplasmic release by treatment of thewashed and resuspended cell pellet with 2% v/v dichloromethane in 50 mMTris buffer pH 8. The lysate was separated from cell debris bycentrifugation and further processed by concentration using an Amiconultrafilter fitted with a 10,000 Dalton membrane. The concentratedlysate may be used in assays directly or the enzyme can be furtherpurified by metal ion affinity chromatography using the engineered 6×poly histidine tag on the C-terminus of the enzyme (SEQ ID NO: 137).

Example 19 Solid Phase Trehalose Production

A solid composite fabric covered hydrophilic foam composed of asubstrate foam used as a media/moisture reservoir (Foamex Aquazone) wasbound to a fabric layer (DuPont Sontara) used as a growth surfacemeasuring 15 cm by 15 cm. The composite material was sterilized bysoaking in 70% ethanol in water and then hung in a vertical bioreactorplumbed to deliver solutions to the top of the composite material. Thesolutions were allowed to percolate through the growing compositesurface by gravity. Residual ethanol was removed from the sterilizedgrowing surface by passage of 1 liter of sterile de-ionized waterflowing at 0.2 ml/min. The growing surface was equilibrated with culturemedia by flowing 0.5 liters of BG11A growth medium containing 10micrograms/ml chloramphenicol through the composite material at 0.2ml/min.

The equilibrated, sterile growth surface was inoculated by flooding thesurface with 10 ml of a 4 day pre-culture of Synechocystis spp. PCC 6803transformed by plasmid pLYBAL23. Following 30 minute incubation thereactor was turned to a vertical position and the fermentation wasbegun. The reactor was illuminated with 80 microeisteins of light from awhite LED array. Temperature was maintained at 28° C., by a resistiveheating device attached to the bioreactor. The reactor was continuouslypurged with 0.2 micron filtered air at 0.2 L/min and fresh culture mediawas supplied by pump and gravity percolation through the foam layer ofthe growth composite at a rate of 0.2 ml/min for 30 minutes every 6hours. The reactor was run continuously for 4-7 days during which thegrowth surface of the composite was overspread with a dense lawn ofcyanobacteria. Following the initial cultivation period the temperatureof the bioreactor was increased to 40° C. and maintained at thistemperature for an additional 24 hours. During the elevated temperatureperiod spent culture broth was collected and processed for trehalosedetermination. At the completion of the fermentation run the biomass wascollected by rinsing the growth surface with de-ionized water which canbe processed for trehalose assay.

The amount of trehalose produced and retained in the biomass grown onthe solid surface was up to 2.5 wt % of the total dry weight biomassrecovered from the bioreactor following temperature induction. 0.8 wt %of the dry biomass equivalent weight of trehalose was recovered from theculture medium following temperature induction.

Example 20 Trehalose Production Liquid Phase

1 liter of sterile BG11A media was prepared in a Bioflow reactor towhich chloramphenicol was added to a concentration of 10 micrograms/ml.The reactor was then inoculated with a 5% by volume, 4 day pre-cultureof Synechocystis spp. PCC 6803 transformed with plasmid pLYBAL23. Thereactor was run at 28° C., 300 RPM, 0.2 L/min 0.2 micron filtered airpurge and illuminated at 80 microeinsteins of light using a fluorescentbulb array. The cultivation was maintained for 4-7 days following whicha 200 ml sample was removed for processing and trehalose assay. Thetemperature of the fermentation was then elevated to 40° C. for 24hours. A 200 ml sample was then removed from the bioreactor forprocessing and trehalose assay.

Following temperature induction the dried biomass produced up to 3 wt %trehalose while the spent culture broth contained 0.3 wt % trehaloseequivalent relative to biomass.

REFERENCES

All publications, patents, patent applications, and other referencescited in this application are incorporated herein by reference in theirentirety for all purposes to the same extent as if each individualpublication, patent, patent application or other reference wasspecifically and individually indicated to be incorporated by referencein its entirety for all purposes. Citation of a reference herein shallnot be construed as an admission that such is prior art to the presentinvention.

1. A device for cultivating photosynthetic microorganisms, comprising; astructure comprising a base, an axial support, and a plurality ofsuspension elements; the base maintaining the axial support in asubstantially horizontal position; the plurality of suspension elementsextending radially from and perpendicular to the axial support such thatthe axial support and plurality of suspension elements define a hub andspoke structure; wherein the axial support is configured to rotate withrespect to the base and the plurality of suspension elements areconfigured to rotate around the axis defined by the axial support; aplurality of solid, non-gelatinous cultivation supports, (i) each of theplurality of cultivation supports coupled to and positioned between atleast two of the plurality of suspension elements, each of the pluralityof cultivation supports extending substantially vertically with respectto the base and configured to maintain a substantially vertical positionupon rotation of the plurality of suspension elements around the axisdefined by the axial support; or (ii) each of the plurality ofcultivation supports coupled to and positioned between at least two ofthe plurality of suspension elements, such that upon rotation of each ofthe plurality of suspension elements around the axis defined by theaxial support, each of the cultivation supports is configured totransition between substantially horizontal and substantially verticalorientations; and a physical barrier disposed over at least a portion ofthe plurality of cultivation supports.
 2. The device according to claim1, wherein a volume of air separates at least a portion of the barrierlayer from at least a portion of the plurality of cultivation supports.3. The device according to claim 1, wherein the plurality of suspensionelements are configured to rotate the plurality of cultivation supportsaround the axis defined by the axial support so as to optimize lightabsorbance for each of the cultivation supports.
 4. The device accordingto claim 1, further comprising a spray device for distributing a liquidmedium over the plurality of cultivation supports.
 5. The deviceaccording to claim 4, wherein the spray device is disposed between thebarrier layer and the plurality of cultivation supports.
 6. The deviceaccording to claim 1, wherein the physical barrier is disposed over atleast a portion of the plurality of cultivation supports or at least aportion of the plurality of suspension elements or the structure.
 7. Thedevice according to claim 1, wherein the physical barrier is releasablysealed so as to enclose the plurality of cultivation supports.
 8. Thedevice according to claim 1, wherein the physical barrier, or a portionthereof, is substantially transparent to actinic irradiation.
 9. Thedevice according to claim 1, wherein the physical barrier, or a portionthereof, is (i) substantially impermeable to solid particulate orliquid, and (ii) partially or substantially permeable to gas or vapor.10. The device according to claim 1, wherein the physical barrier, or aportion thereof, is a flexible physical barrier.
 11. The deviceaccording to claim 1, wherein the physical barrier comprises a firstbarrier portion and a second barrier portion, wherein the first barrierportion and the second barrier portion are different with respect to oneor more of liquid permeability, gas permeability, or transparency toactinic radiation.
 12. The device according to claim 1, wherein each ofthe cultivation supports has a sheet shape, and a depth of each of thecultivation supports is substantially less than a length and a width ofsuch cultivation support.
 13. The device according to claim 1, whereinthe plurality of cultivation supports comprise a textured surfacesuitable for adherence of a photosynthetic microorganism.
 14. The deviceaccording to claim 1, wherein the plurality of cultivation supportscomprise a non-gelatinous, textured surface suitable for culturingphotosynthetic microorganisms at a density of at least about 50 grams ofdry biomass per liter equivalent.
 15. The device according to claim 1,wherein the plurality of cultivation supports comprises: (i) a fabriccomprising a natural, modified natural, or synthetic fiber, or acombination thereof; (ii) a fabric comprising a woven fabric, a knittedfabric, a felt, a mesh of cross-linked fiber polymers, or a combinationthereof; (iii) a fabric comprising natural fibers selected from thegroup consisting of cotton, wool, hemp, tree fiber, other cellulosicfibers, and combinations thereof; (iv) a fabric comprising modifiednatural fibers selected from the group consisting of nitrocellulose,cellulose acetate, cellulose sulfonate, crosslinked starches, andcombinations thereof; (v) a fabric comprising synthetic fibers selectedfrom the group consisting of polyester, polyacrylate, polyamine,polyamide, polysulfone, and combinations thereof; (vi) a material havingloops; (vii) a material having loops, the material being terry cloth; or(viii) a combination thereof.
 16. The device according to claim 1,wherein the plurality of cultivation supports comprise: (i) a flexiblematerial, (ii) a rigid material, or (iii) flexibly connected rigidportions, wherein the rigid portions are comprised of a rigid material.17. The device according to claim 1, wherein each of the plurality ofcultivation supports further comprises a coating of a moisture absorbentpolymer selected from the group consisting of agar, polyacrylate,polyamide, polyamine, polyethylene glycol, modified starches, andcombinations thereof.
 18. The device according to claim 1, furthercomprising water, nutrients, or a combination thereof on or within eachof the plurality of cultivation supports.
 19. The device according toclaim 1, further comprising: at least one of a fluid supply system,nutrient supply system, gas supply system, or microorganism supplysystem.
 20. The device according to claim 1, wherein each of theplurality of suspension elements comprises one or more attachment pointsfor attaching a corresponding cultivation support.
 21. The deviceaccording to claim 1, wherein each of the cultivation supports ispositioned substantially horizontally between at least two of theplurality of suspension elements.